Full wwpdb NMR Structure Validation Report

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1 Full wwpdb NMR Structure Validation Report io Apr 14, :51 PM EDT PDB ID : 2J0Z Title : p53 tetramerization domain wild type Authors : Carbajo, R.J.; Mora, P.; Sanchez del Pino, M.M.; Perez-Paya, E.; Pineda- Lucena, A. Deposited on : This is a Full wwpdb NMR Structure Validation Report for a publicly released PDB entry. We welcome your comments at validation@mail.wwpdb.org A user guide is available at with specic help available everywhere you see the io symbol. The following versions of software and data (see references io) were used in the production of this report: Cyrange : Kirchner and Güntert (2011) NmrClust : Kelley et al. (1996) MolProbity : 4.02b-467 Percentile statistics : v01 (using entries in the PDB archive December 27th 2017) RCI : v_1n_11_5_13_a (Berjanski et al., 2005) PANAV : Wang et al. (2010) ShiftChecker : rb Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et al. (1996) Validation Pipeline (wwpdb-vp) : rb

Page 2 Full wwpdb NMR Structure Validation Report 2J0Z 1 Overall quality at a glance io The following experimental techniques were used to determine the structure: SOLUTION NMR The overall

The table shows the number of entries on which the scores are based.

2 Page 2 Full wwpdb NMR Structure Validation Report 2J0Z 1 Overall quality at a glance io The following experimental techniques were used to determine the structure: SOLUTION NMR The overall completeness of chemical shifts assignment was not calculated. Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in the following graphic. The table shows the number of entries on which the scores are based. Metric Whole archive NMR archive (#Entries) (#Entries) Clashscore Ramachandran outliers Sidechain outliers The table below summarises the geometric issues observed across the polymeric chains and their t to the experimental data. The red, orange, yellow and green segments indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A cyan segment indicates the fraction of residues that are not part of the well-dened cores, and a grey segment represents the fraction of residues that are not modelled. The numeric value for each fraction is indicated below the corresponding segment, with a dot representing fractions <=5% Mol Chain Length Quality of chain 1 A 31 1 B 31 1 C 31 1 D 31

3 Page 3 Full wwpdb NMR Structure Validation Report 2J0Z 2 Ensemble composition and analysis io This entry contains 30 models. Model 18 is the overall representative, medoid model (most similar to other models). The authors have identied model 17 as representative. The following residues are included in the computation of the global validation metrics. Well-dened (core) protein residues Well-dened core Residue range (total) Backbone RMSD (Å) Medoid model 1 A:327-A:354, B:327-B:354, C:327-C:354, D:327-D:354 (112) Ill-dened regions of proteins are excluded from the global statistics. Ligands and non-protein polymers are included in the analysis. The models can be grouped into 3 clusters and 2 single-model clusters were found. Cluster number Models 1 1, 2, 4, 5, 8, 9, 11, 13, 15, 16, 17, 18, 20, 24, 26, , 6, 7, 12, 19, 23, 25, 29, , 21, 27 Single-model clusters 14; 22

4 Page 4 Full wwpdb NMR Structure Validation Report 2J0Z 3 Entry composition io There is only 1 type of molecule in this entry. The entry contains 2088 atoms, of which 1028 are hydrogens and 0 are deuteriums. ˆ Molecule 1 is a protein called CELLULAR TUMOR ANTIGEN P53. Mol Chain Residues Atoms Trace 1 A 31 Total C H N O S B 31 Total C H N O S C 31 Total C H N O S D 31 Total C H N O S

5 Page 5 Full wwpdb NMR Structure Validation Report 2J0Z 4 Residue-property plots io 4.1 Average score per residue in the NMR ensemble These plots are provided for all protein, RNA and DNA chains in the entry. The rst graphic is the same as shown in the summary in section 1 of this report. The second graphic shows the sequence where residues are colour-coded according to the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretches of 2 or more consecutive residues without any outliers are shown as green connectors. Residues which are classied as ill-dened in the NMR ensemble, are shown in cyan with an underline colour-coded according to the previous scheme. Residues which were present in the experimental sample, but not modelled in the nal structure are shown in grey. 4.2 Scores per residue for each member of the ensemble Colouring as in section 4.1 above Score per residue for model 1

6 Page 6 Full wwpdb NMR Structure Validation Report 2J0Z Score per residue for model 2

7 Page 7 Full wwpdb NMR Structure Validation Report 2J0Z G Score per residue for model 3 G Score per residue for model 4

8 Page 8 Full wwpdb NMR Structure Validation Report 2J0Z Q Score per residue for model 5 G334 Q354

9 Page 9 Full wwpdb NMR Structure Validation Report 2J0Z Score per residue for model 6 G Score per residue for model 7

10 Page 10 Full wwpdb NMR Structure Validation Report 2J0Z Score per residue for model Score per residue for model 9

11 Page 11 Full wwpdb NMR Structure Validation Report 2J0Z Q354 Q Score per residue for model 10

12 Page 12 Full wwpdb NMR Structure Validation Report 2J0Z Score per residue for model Score per residue for model 12

13 Page 13 Full wwpdb NMR Structure Validation Report 2J0Z G334 A353 Q Score per residue for model 13 A353 Q Score per residue for model 14 Q354

14 Page 14 Full wwpdb NMR Structure Validation Report 2J0Z Score per residue for model 15

15 Page 15 Full wwpdb NMR Structure Validation Report 2J0Z Score per residue for model 16 G Score per residue for model 17

16 Page 16 Full wwpdb NMR Structure Validation Report 2J0Z Q354 G Score per residue for model 18 (medoid) Score per residue for model 19 G334

17 Page 17 Full wwpdb NMR Structure Validation Report 2J0Z Q354 Q Score per residue for model 20 Q354 G334

18 Page 18 Full wwpdb NMR Structure Validation Report 2J0Z Score per residue for model Score per residue for model 22 Q354

19 Page 19 Full wwpdb NMR Structure Validation Report 2J0Z Score per residue for model Score per residue for model 24 G334

20 Page 20 Full wwpdb NMR Structure Validation Report 2J0Z G Score per residue for model 25

21 Page 21 Full wwpdb NMR Structure Validation Report 2J0Z Score per residue for model Score per residue for model 27 Q354

22 Page 22 Full wwpdb NMR Structure Validation Report 2J0Z G Score per residue for model Score per residue for model 29 A353 Q354

23 Page 23 Full wwpdb NMR Structure Validation Report 2J0Z Score per residue for model 30 Q354 Q354

24 Page 24 Full wwpdb NMR Structure Validation Report 2J0Z 5 Renement protocol and experimental data overview io The models were rened using the following method: CNS. Of the 30 calculated structures, 30 were deposited, based on the following criterion: ENERGY. The following table shows the software used for structure solution, optimisation and renement. Software name Classication Version CNS renement SPARKY structure solution TOTAL No chemical shift data was provided. No validations of the models with respect to experimental NMR restraints is performed at this time.

25 Page 25 Full wwpdb NMR Structure Validation Report 2J0Z 6 Model quality io 6.1 Standard geometry io There are no covalent bond-length or bond-angle outliers. There are no bond-length outliers. There are no bond-angle outliers. There are no chirality outliers. There are no planarity outliers. 6.2 Too-close contacts io In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms and hydrogen atoms in each chain respectively. The H(added) column lists the number of hydrogen atoms added and optimized by MolProbity. The Clashes column lists the number of clashes averaged over the ensemble. Mol Chain Non-H H(model) H(added) Clashes 1 A ±2 1 B ±3 1 C ±3 1 D ±2 All All The all-atom clashscore is dened as the number of clashes found per 1000 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 12. All unique clashes are listed below, sorted by their clash magnitude. Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 1:C:330:LEU:HD23 1:C:332:ILE:HD :B:330:LEU:HD23 1:B:332:ILE:HD :A:330:LEU:HD23 1:A:332:ILE:HD :B:344:LEU:HD12 1:B:348:LEU:HD :A:344:LEU:HD21 1:D:344:LEU:HD :D:330:LEU:HD23 1:D:332:ILE:HD :B:344:LEU:HD11 1:C:344:LEU:HD :A:344:LEU:HD11 1:D:344:LEU:HD :B:344:LEU:HD11 1:C:344:LEU:CD :A:344:LEU:HD21 1:D:344:LEU:HD :A:344:LEU:CD2 1:D:344:LEU:HD Continued on next page...

26 Page 26 Full wwpdb NMR Structure Validation Report 2J0Z Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 1:D:330:LEU:HD12 1:D:332:ILE:HD :B:330:LEU:CD2 1:B:332:ILE:HD :B:344:LEU:HD21 1:C:344:LEU:HD :C:350:LEU:HD12 1:C:351:LYS:N :C:338:PHE:CE2 1:D:330:LEU:HD :C:330:LEU:CD2 1:C:332:ILE:HD :A:330:LEU:HD13 1:B:338:PHE:CE :C:337:ARG:HD2 1:D:348:LEU:HD :B:344:LEU:HD21 1:C:344:LEU:HD :C:344:LEU:O 1:C:348:LEU:HD :C:348:LEU:HD13 1:D:337:ARG:CG :D:344:LEU:O 1:D:348:LEU:HD :A:338:PHE:CE1 1:B:330:LEU:HD :A:344:LEU:O 1:A:348:LEU:HD :D:350:LEU:HD12 1:D:351:LYS:N :D:330:LEU:CD1 1:D:332:ILE:HD :B:344:LEU:O 1:B:348:LEU:HD :C:338:PHE:CZ 1:D:330:LEU:HD :A:344:LEU:HD21 1:D:344:LEU:CD :A:338:PHE:CE2 1:B:330:LEU:HD :A:344:LEU:O 1:A:348:LEU:HD :A:348:LEU:HD13 1:B:337:ARG:HG :A:330:LEU:HD13 1:B:338:PHE:CE :C:348:LEU:HD22 1:D:337:ARG:HG :C:338:PHE:CE1 1:D:330:LEU:HD :A:329:THR:HG23 1:B:331:GLN:HG :D:344:LEU:O 1:D:348:LEU:HD :B:344:LEU:HD11 1:C:344:LEU:HD :C:337:ARG:CD 1:D:348:LEU:HD :A:347:ALA:HB1 1:D:347:ALA:HB :A:348:LEU:HD13 1:B:337:ARG:HD :A:344:LEU:HD23 1:D:344:LEU:HD :A:344:LEU:HD21 1:D:344:LEU:HD :B:347:ALA:HB1 1:C:347:ALA:HB :A:350:LEU:HD12 1:A:351:LYS:N :A:338:PHE:CZ 1:B:330:LEU:HD :B:344:LEU:CD2 1:C:344:LEU:HD :B:344:LEU:O 1:B:348:LEU:HD :B:344:LEU:HD22 1:C:344:LEU:HD :A:348:LEU:HD13 1:A:351:LYS:HD :B:344:LEU:O 1:B:348:LEU:HD Continued on next page...

27 Page 27 Full wwpdb NMR Structure Validation Report 2J0Z Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 1:B:344:LEU:CD2 1:C:344:LEU:HD :A:337:ARG:NE 1:B:348:LEU:HD :B:344:LEU:HD12 1:B:348:LEU:CD :A:331:GLN:HG3 1:B:329:THR:HG :A:337:ARG:CG 1:B:348:LEU:HD :A:338:PHE:CE1 1:B:330:LEU:HD :A:337:ARG:HG3 1:B:348:LEU:HD :C:329:THR:HG23 1:D:331:GLN:HG :B:344:LEU:HD21 1:C:344:LEU:HG :B:344:LEU:CG 1:C:344:LEU:HD :C:330:LEU:HD13 1:D:338:PHE:CE :A:344:LEU:HD11 1:D:344:LEU:HD :B:346:GLU:O 1:B:350:LEU:HD :C:330:LEU:HD12 1:D:338:PHE:CD :A:346:GLU:O 1:A:350:LEU:HD :C:337:ARG:CG 1:D:348:LEU:HD :D:348:LEU:HD13 1:D:351:LYS:HD :C:337:ARG:HG2 1:D:348:LEU:HD :C:338:PHE:CE1 1:D:330:LEU:HD :A:330:LEU:HG 1:A:332:ILE:HD :A:344:LEU:HD22 1:D:344:LEU:HD :B:344:LEU:HD21 1:C:344:LEU:CG :A:348:LEU:HD13 1:B:337:ARG:HD :C:337:ARG:HG2 1:D:348:LEU:HD :C:348:LEU:HD13 1:D:337:ARG:HG :A:348:LEU:HD13 1:B:337:ARG:CG :B:344:LEU:HG 1:C:344:LEU:HD :A:337:ARG:HG3 1:B:348:LEU:HD :C:337:ARG:NE 1:D:348:LEU:HD :B:348:LEU:HD13 1:B:351:LYS:HD :B:344:LEU:HD21 1:C:344:LEU:CD :D:330:LEU:CD2 1:D:332:ILE:HD :A:345:ASN:ND2 1:B:332:ILE:HD :C:330:LEU:HD13 1:D:338:PHE:CE :B:344:LEU:HD21 1:C:344:LEU:HD :B:344:LEU:HD22 1:C:344:LEU:CD :D:346:GLU:O 1:D:350:LEU:HD :A:344:LEU:CG 1:D:344:LEU:HD :C:331:GLN:HG3 1:D:329:THR:HG :A:344:LEU:HD21 1:D:344:LEU:HG :A:332:ILE:HG23 1:B:345:ASN:OD Continued on next page...

28 Page 28 Full wwpdb NMR Structure Validation Report 2J0Z Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 1:A:337:ARG:NE 1:B:348:LEU:HD :B:344:LEU:HD22 1:C:344:LEU:HD :B:351:LYS:CE 1:C:347:ALA:HB :A:330:LEU:CD2 1:A:332:ILE:HD :C:331:GLN:HG2 1:D:329:THR:HG :C:348:LEU:HD13 1:D:337:ARG:HD :B:343:GLU:OE2 1:C:348:LEU:HD :C:344:LEU:O 1:C:348:LEU:HD :C:331:GLN:CG 1:D:329:THR:HG :C:332:ILE:HG23 1:D:345:ASN:OD :A:350:LEU:HD23 1:D:354:GLN:OE :C:346:GLU:O 1:C:350:LEU:HD :B:344:LEU:HD11 1:C:344:LEU:HD :C:348:LEU:HD13 1:D:337:ARG:HB :B:346:GLU:OE1 1:B:350:LEU:HD :A:348:LEU:HD12 1:B:337:ARG:HD :A:344:LEU:HG 1:D:344:LEU:HD :C:329:THR:CG2 1:D:329:THR:HG :B:344:LEU:CD1 1:C:344:LEU:HD :B:332:ILE:HD12 1:B:332:ILE:N :A:337:ARG:HD3 1:B:348:LEU:HD :B:332:ILE:HG21 1:B:337:ARG:HB :C:348:LEU:HD13 1:C:351:LYS:HD :A:348:LEU:HD23 1:A:351:LYS:HD :A:346:GLU:O 1:A:350:LEU:HD :C:348:LEU:HD13 1:D:337:ARG:HG :A:344:LEU:CD2 1:D:344:LEU:HD :C:345:ASN:OD1 1:D:332:ILE:HG :C:330:LEU:O 1:C:332:ILE:HD :B:348:LEU:HD23 1:B:351:LYS:HD :A:332:ILE:HD12 1:A:332:ILE:N :B:350:LEU:HD22 1:C:354:GLN:NE :B:344:LEU:CD1 1:C:344:LEU:HD :A:330:LEU:O 1:A:332:ILE:HD :A:332:ILE:HD13 1:A:341:PHE:CD :C:340:MET:O 1:C:344:LEU:HD :A:337:ARG:CD 1:B:348:LEU:HD :A:348:LEU:HD13 1:B:337:ARG:HG :A:344:LEU:HD11 1:D:344:LEU:HD :A:344:LEU:HD21 1:D:344:LEU:CG :D:332:ILE:HG21 1:D:337:ARG:HG Continued on next page...

29 Page 29 Full wwpdb NMR Structure Validation Report 2J0Z Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 1:A:345:ASN:OD1 1:B:332:ILE:HG :C:348:LEU:HD23 1:C:351:LYS:HD :A:348:LEU:HD13 1:B:337:ARG:CD :B:351:LYS:HD2 1:C:347:ALA:HB :C:330:LEU:HD12 1:D:338:PHE:CE :C:337:ARG:HD2 1:D:348:LEU:HD :A:332:ILE:HG23 1:A:337:ARG:CZ :C:337:ARG:HD3 1:D:348:LEU:HD :B:332:ILE:N 1:B:332:ILE:HD :B:344:LEU:HD11 1:C:344:LEU:CG :B:331:GLN:C 1:B:332:ILE:HD :A:329:THR:HG22 1:B:329:THR:CG :C:337:ARG:HG3 1:D:348:LEU:HD :A:337:ARG:HD2 1:B:348:LEU:HD :D:332:ILE:HG23 1:D:337:ARG:CZ :C:340:MET:CE 1:D:348:LEU:HD :C:329:THR:HG22 1:D:329:THR:HG :D:340:MET:O 1:D:344:LEU:HD :B:344:LEU:HD22 1:C:344:LEU:HD :A:341:PHE:CD1 1:B:341:PHE:CD :A:337:ARG:HG2 1:B:348:LEU:HD :A:340:MET:O 1:A:344:LEU:HD :C:332:ILE:HG23 1:D:345:ASN:ND :C:348:LEU:HD13 1:D:337:ARG:HD :B:351:LYS:NZ 1:C:347:ALA:HB :A:337:ARG:HD2 1:B:348:LEU:HD :C:341:PHE:CD1 1:D:341:PHE:CD :C:332:ILE:HG23 1:D:345:ASN:HD :A:350:LEU:HD12 1:A:350:LEU:C :D:350:LEU:HD12 1:D:350:LEU:C :B:347:ALA:CB 1:C:347:ALA:HB :A:337:ARG:CZ 1:B:348:LEU:HD :A:330:LEU:HD12 1:B:338:PHE:CE :A:330:LEU:N 1:A:330:LEU:HD :D:330:LEU:O 1:D:332:ILE:HD :C:341:PHE:CD2 1:D:341:PHE:CD :A:344:LEU:HD21 1:D:344:LEU:CD :A:347:ALA:HB2 1:D:351:LYS:NZ :B:344:LEU:CD2 1:C:344:LEU:HD :A:341:PHE:CD2 1:B:341:PHE:CD :B:340:MET:O 1:B:344:LEU:HD Continued on next page...

30 Page 30 Full wwpdb NMR Structure Validation Report 2J0Z Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 1:C:346:GLU:O 1:C:350:LEU:HD :D:346:GLU:O 1:D:350:LEU:HD :A:337:ARG:CG 1:B:348:LEU:HD :C:345:ASN:ND2 1:D:332:ILE:HG :B:350:LEU:C 1:B:350:LEU:HD :C:350:LEU:HD12 1:C:350:LEU:C :B:351:LYS:HE3 1:C:347:ALA:HB :C:331:GLN:HG3 1:D:329:THR:HG :D:350:LEU:C 1:D:350:LEU:HD :B:344:LEU:HD22 1:C:344:LEU:CD :C:341:PHE:CD1 1:D:341:PHE:CD :A:344:LEU:HD11 1:D:344:LEU:CD :C:348:LEU:HD13 1:D:337:ARG:NE :B:347:ALA:HB2 1:C:351:LYS:HE :C:348:LEU:HD13 1:D:337:ARG:CD :A:351:LYS:CE 1:D:347:ALA:HB :A:337:ARG:HB3 1:B:348:LEU:HD :C:332:ILE:HD13 1:C:341:PHE:CD :A:337:ARG:CD 1:B:348:LEU:HD :A:329:THR:HG22 1:B:329:THR:HG :A:340:MET:CE 1:B:344:LEU:HD :C:341:PHE:CD2 1:D:341:PHE:CD :A:329:THR:CG2 1:B:329:THR:HG :B:330:LEU:O 1:B:332:ILE:HD :C:345:ASN:HD21 1:D:332:ILE:HG :A:331:GLN:HG3 1:B:329:THR:HG :A:348:LEU:HD13 1:A:351:LYS:HD :C:338:PHE:CD2 1:D:328:PHE:CB :B:346:GLU:O 1:B:350:LEU:HD :A:345:ASN:ND2 1:B:330:LEU:HD :C:330:LEU:CD1 1:D:338:PHE:CE :C:332:ILE:HG21 1:C:337:ARG:HD :B:347:ALA:HB2 1:C:351:LYS:HE :C:333:ARG:CD 1:D:327:TYR:CE :C:337:ARG:HG3 1:C:341:PHE:CE :B:344:LEU:HD21 1:C:344:LEU:CD :A:338:PHE:CD2 1:B:328:PHE:CB :C:333:ARG:CG 1:D:327:TYR:CE :C:330:LEU:HG 1:C:332:ILE:HD :C:348:LEU:HD12 1:D:337:ARG:CG :A:351:LYS:HE3 1:D:347:ALA:HB Continued on next page...

31 Page 31 Full wwpdb NMR Structure Validation Report 2J0Z Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 1:A:347:ALA:HB2 1:D:351:LYS:CE :C:329:THR:HG22 1:D:329:THR:CG :A:337:ARG:HG3 1:A:341:PHE:CE :C:337:ARG:HG3 1:C:341:PHE:CE :C:328:PHE:CD1 1:C:328:PHE:N :A:347:ALA:HB2 1:D:351:LYS:HE :A:330:LEU:CD1 1:B:338:PHE:CE :C:327:TYR:CE1 1:D:333:ARG:CG :C:338:PHE:CE2 1:D:330:LEU:CD :C:341:PHE:CD2 1:C:341:PHE:N :B:330:LEU:CG 1:B:332:ILE:HD :A:328:PHE:CD1 1:A:328:PHE:N :A:332:ILE:HG21 1:A:337:ARG:HG :A:341:PHE:CD2 1:B:341:PHE:CD :A:330:LEU:HD22 1:B:338:PHE:CD :A:330:LEU:HD12 1:B:338:PHE:CE :A:344:LEU:HD22 1:D:344:LEU:HD :B:328:PHE:N 1:B:328:PHE:CD :A:330:LEU:HD13 1:B:338:PHE:CZ :A:338:PHE:CE2 1:B:330:LEU:HD :B:341:PHE:N 1:B:341:PHE:CD :C:330:LEU:CG 1:C:332:ILE:HD :B:332:ILE:HD13 1:B:341:PHE:CE :A:335:ARG:CD 1:B:328:PHE:CZ :B:328:PHE:CD2 1:B:328:PHE:N :B:350:LEU:HD23 1:C:354:GLN:OE :B:344:LEU:HD11 1:C:344:LEU:CD :A:344:LEU:HD21 1:D:344:LEU:HD :A:341:PHE:CD1 1:B:341:PHE:CD :B:344:LEU:CD1 1:C:344:LEU:HD :B:337:ARG:HG2 1:B:341:PHE:CE :A:337:ARG:HG3 1:A:341:PHE:CE :D:337:ARG:HG2 1:D:341:PHE:CE :C:348:LEU:HD11 1:D:337:ARG:HD :A:328:PHE:CB 1:B:338:PHE:CD :B:337:ARG:HG3 1:B:341:PHE:CE :A:330:LEU:HD13 1:B:338:PHE:HE :D:332:ILE:HG21 1:D:341:PHE:CE :C:333:ARG:CG 1:D:327:TYR:CZ :A:337:ARG:NH2 1:B:348:LEU:HD :A:330:LEU:HD22 1:A:332:ILE:HD Continued on next page...

32 Page 32 Full wwpdb NMR Structure Validation Report 2J0Z Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 1:C:328:PHE:CD2 1:C:328:PHE:N :A:351:LYS:HG3 1:D:350:LEU:HD :C:338:PHE:CD1 1:D:330:LEU:HD :A:354:GLN:NE2 1:D:350:LEU:HD :C:327:TYR:O 1:C:328:PHE:CD :D:328:PHE:CD1 1:D:328:PHE:N :A:344:LEU:CD2 1:D:344:LEU:CD :A:333:ARG:CG 1:B:327:TYR:CE :B:337:ARG:HG3 1:B:341:PHE:CE :B:328:PHE:CD1 1:B:328:PHE:N :C:329:THR:HG23 1:D:331:GLN:HG :D:328:PHE:CD2 1:D:328:PHE:N :C:328:PHE:N 1:C:328:PHE:CD :B:348:LEU:HD13 1:B:351:LYS:HD :B:332:ILE:N 1:B:332:ILE:CD :A:347:ALA:CB 1:D:351:LYS:CE :A:332:ILE:HG23 1:B:345:ASN:ND Torsion angles io Protein backbone io In the following table, the Percentiles column shows the percent Ramachandran outliers of the chain as a percentile score with respect to all PDB entries followed by that with respect to all NMR entries. The Analysed column shows the number of residues for which the backbone conformation was analysed and the total number of residues. Mol Chain Analysed Favoured Allowed Outliers Percentiles 1 A 28/31 (90%) 27±1 (96±3%) 1±1 (3±2%) 0±0 (1±2%) B 28/31 (90%) 27±1 (95±3%) 1±1 (3±3%) 1±1 (2±2%) C 28/31 (90%) 26±1 (94±4%) 1±1 (4±4%) 1±1 (2±2%) D 28/31 (90%) 26±1 (94±4%) 1±1 (4±3%) 0±1 (2±2%) All All 3360/3720 (90%) 3182 (95%) 124 (4%) 54 (2%) All 6 unique Ramachandran outliers are listed below. They are sorted by the frequency of occurrence in the ensemble. Mol Chain Res Type Models (Total) 1 B 327 TYR 15 Continued on next page...

33 Page 33 Full wwpdb NMR Structure Validation Report 2J0Z Continued from previous page... Mol Chain Res Type Models (Total) 1 C 327 TYR 14 1 D 327 TYR 13 1 A 327 TYR 10 1 D 334 GLY 1 1 C 329 THR Protein sidechains io In the following table, the Percentiles column shows the percent sidechain outliers of the chain as a percentile score with respect to all PDB entries followed by that with respect to all NMR entries. The Analysed column shows the number of residues for which the sidechain conformation was analysed and the total number of residues. Mol Chain Analysed Rotameric Outliers Percentiles 1 A 25/26 (96%) 21±2 (84±6%) 4±2 (16±6%) B 25/26 (96%) 21±2 (82±7%) 4±2 (18±7%) C 25/26 (96%) 21±2 (84±7%) 4±2 (16±7%) D 25/26 (96%) 21±1 (83±6%) 4±1 (17±6%) 5 41 All All 3000/3120 (96%) 2502 (83%) 498 (17%) 6 42 All 81 unique residues with a non-rotameric sidechain are listed below. They are sorted by the frequency of occurrence in the ensemble. Mol Chain Res Type Models (Total) 1 B 329 THR 19 1 D 329 THR 18 1 C 329 THR 17 1 A 329 THR 15 1 C 344 LEU 14 1 C 342 ARG 14 1 D 344 LEU 13 1 B 342 ARG 13 1 A 344 LEU 13 1 B 344 LEU 12 1 A 342 ARG 12 1 B 337 ARG 11 1 A 333 ARG 11 1 D 351 LYS 11 1 C 335 ARG 11 1 D 335 ARG 10 Continued on next page...

34 Page 34 Full wwpdb NMR Structure Validation Report 2J0Z Continued from previous page... Mol Chain Res Type Models (Total) 1 C 333 ARG 10 1 B 333 ARG 10 1 A 337 ARG 10 1 D 342 ARG 10 1 B 351 LYS 9 1 D 339 GLU 9 1 B 335 ARG 9 1 A 350 LEU 8 1 B 350 LEU 8 1 D 337 ARG 8 1 A 351 LYS 7 1 A 352 ASP 7 1 C 346 GLU 7 1 B 343 GLU 6 1 A 335 ARG 6 1 D 350 LEU 6 1 C 352 ASP 6 1 D 352 ASP 6 1 C 337 ARG 5 1 B 348 LEU 5 1 B 339 GLU 5 1 A 354 GLN 5 1 C 349 GLU 5 1 D 343 GLU 5 1 C 339 GLU 5 1 D 331 GLN 5 1 B 340 MET 5 1 B 336 GLU 4 1 D 336 GLU 4 1 D 349 GLU 4 1 D 348 LEU 4 1 B 331 GLN 4 1 C 351 LYS 4 1 A 348 LEU 4 1 D 333 ARG 4 1 B 346 GLU 4 1 C 340 MET 4 1 C 350 LEU 3 1 A 346 GLU 3 1 C 345 ASN 3 1 A 339 GLU 3 1 C 343 GLU 3 Continued on next page...

35 Page 35 Full wwpdb NMR Structure Validation Report 2J0Z Continued from previous page... Mol Chain Res Type Models (Total) 1 B 354 GLN 3 1 D 340 MET 3 1 A 349 GLU 2 1 C 348 LEU 2 1 B 349 GLU 2 1 C 331 GLN 2 1 D 345 ASN 2 1 D 354 GLN 2 1 C 336 GLU 2 1 A 340 MET 2 1 A 345 ASN 2 1 D 327 TYR 2 1 A 331 GLN 2 1 B 327 TYR 2 1 C 327 TYR 2 1 C 354 GLN 2 1 A 343 GLU 2 1 A 327 TYR 1 1 B 345 ASN 1 1 D 330 LEU 1 1 A 336 GLU 1 1 A 330 LEU 1 1 B 352 ASP RNA io There are no RNA molecules in this entry. 6.4 Non-standard residues in protein, DNA, RNA chains io There are no non-standard protein/dna/rna residues in this entry. 6.5 Carbohydrates io There are no carbohydrates in this entry. 6.6 Ligand geometry io There are no ligands in this entry.

36 Page 36 Full wwpdb NMR Structure Validation Report 2J0Z 6.7 Other polymers io There are no such molecules in this entry. 6.8 Polymer linkage issues io There are no chain breaks in this entry.

37 Page 37 Full wwpdb NMR Structure Validation Report 2J0Z 7 Chemical shift validation io No chemical shift data were provided

Full wwpdb NMR Structure Validation Report i

Full wwpdb NMR Structure Validation Report i Feb 20, 2018 04:45 am GMT PDB ID : 1DV9 Title : STRUCTURAL CHANGES ACCOMPANYING PH-INDUCED DISSOCIA- TION OF THE B-LACTOGLOBULIN DIMER Authors : Uhrinova, S.;