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1 advances.sciencemag.org/cgi/content/full/2/9/e /dc1 Supplementary Materials for Native phasing of x-ray free-electron laser data for a G protein coupled receptor Alexander Batyuk, Lorenzo Galli, Andrii Ishchenko, Gye Won Han, Cornelius Gati, Petr A. Popov, Ming-Yue Lee, Benjamin Stauch, Thomas A. White, Anton Barty, Andrew Aquila, Mark S. Hunter, Mengning Liang, Sébastien Boutet, Mengchen Pu, Zhi-jie Liu, Garrett Nelson, Daniel James, Chufeng Li, Yun Zhao, John C. H. Spence, Wei Liu, Petra Fromme, Vsevolod Katritch, Uwe Weierstall, Raymond C. Stevens, Vadim Cherezov This PDF file includes: Published 23 September 2016, Sci. Adv. 2, e (2016) DOI: /sciadv fig. S1. A2A-BRIL/ZM microcrystals used for data collection. fig. S2. Strength of anomalous signal and sulfur atom search. fig. S3. Parameter-space screening results for S-SAD phasing using the X 2 DF pipeline. fig. S4. Effect of different data processing methods on data merging metrics. fig. S5. Dependence of anomalous signal measurability on the number of indexed patterns. fig. S6. Final 1.9 Å XFEL room temperature A2AAR-BRIL structure (A2A_S- SAD_1.9). fig. S7. Structure-factor amplitude difference Fourier map between A2A_S- SAD_2.5 and A2A_MR_2.5 structures. fig. S8. B factor comparison between A2A_S-SAD_2.5 and A2A_MR_2.5 structures. fig. S9. Comparison of 2mFo-DFc electron density maps for the ligand- and sodium-binding pockets obtained by S-SAD and MR phasing. fig. S10. C-C difference distance matrix between A2A_S-SAD_1.9 and previously determined A2AAR structure (PDB: 4EIY). fig. S11. B factor comparison between room temperature A2A_S-SAD_1.9 and previously determined cryocooled A2AAR structure (PDB: 4EIY). fig. S12. Distribution of Cys and Met residues in human proteins. table S1. Data collection statistics. table S2. Data refinement statistics.
2 table S3. Comparison of interactions involving charged residues between PDB: 4EIY and A2A_SSAD_1.9 structures. table S4. Comparison of protein and data collection parameters for successful S- SAD phasing of XFEL data.
3 fig. S1. A2A-BRIL/ZM microcrystals used for data collection. The image was taken using a high-resolution zoom stereo microscope with cross-polarizers.
4 fig. S2. Strength of anomalous signal and sulfur atom search. (A) Dependence of the anomalous signal measurability on resolution calculated with phenix.xtriage (31). The anomalous signal measurability, is defined as the fraction of Bijvoet related intensity differences, for which I + -I - /σ(i + -I - ) > 3.0, min[i + /σ(i + ), I - /σ(i - )] > 3.0 holds. (B) SHELXD correlation coefficients, CC, between observed and calculated Bijvoet differences. (C) Sulfur site occupancy vs. peak number plot.
5 fig. S3. Parameter-space screening results for S-SAD phasing using the X 2 DF pipeline. A three-dimensional screening was performed varying the high-resolution limits for the sulfur site search and phasing, and the number of sulfur atoms to search. This figure represents an intersection at the number of sulfur atoms to search of 10. However, SHELXD yielded 18 sites, and 6 low occupancy sites were eliminated automatically before phasing. The results show that there are multiple combinations of high-resolution limits for sulfur site search and phasing which led to structure solutions. Colors represent the respective Rfree value as indicated by the color scalebar. fig. S4. Effect of different data processing methods on data merging metrics. (A) Correlation coefficient CC1/2 and (B) Rsplit factor.
6 fig. S5. Dependence of anomalous signal measurability on the number of indexed patterns. The anomalous signal measurability is calculated by phenix.xtriage (31) in the resolution range Å. The anomalous signal measurability is defined as the fraction of Bijvoet related intensity differences, for which I + -I - /σ(i + -I - ) > 3.0, min[i + /σ(i + ), I - /σ(i - )] > 3.0 holds.
7 fig. S6. Final 1.9 Å XFEL room temperature A2AAR-BRIL structure (A2A_S-SAD_1.9). A2AAR is shown as a pale green cartoon, BRIL fusion as a green cartoon. Ligand ZM is shown as spheres with magenta carbons, cholesterols as spheres with yellow carbons, and other lipids as spheres with gray carbons. The sodium ion is shown as a purple sphere, and water molecules as small blue spheres. The membrane boundaries are indicated by blue lines with the extracellular side on the top and intracellular side on the bottom.
8 fig. S7. Structure-factor amplitude difference Fourier map between A2A_S-SAD_2.5 and A2A_MR_2.5 structures. Electron density is contoured at +3σ (green) and -3σ (red).
9 Normalized B-factor difference B-factor, Ų A Residue number B Residue number fig. S8. B factor comparison between A2A_S-SAD_2.5 and A2A_MR_2.5 structures. (A) Distribution of Cα atom B-factors for A2A_S-SAD_2.5 (red) and A2A_MR_2.5 (blue) vs residue number. (B) Normalized Cα atom B-factor difference between A2A_S-SAD_2.5 and A2A_MR_2.5 structures.
10 fig. S9. Comparison of 2mFo-DFc electron density maps for the ligand- and sodiumbinding pockets obtained by S-SAD and MR phasing. (A), (B) and (C) Ligand binding pocket for A2A_S-SAD_2.5 (A), A2A_MR_2.5 (B) and A2A_S-SAD_1.9 (C) structures. (D), (E) and (F) Sodium ion binding site for A2A_S-SAD_2.5 (D), A2A_MR_2.5 (E) and A2A_S- SAD_1.9 (F) structures. Electron density is contoured at 0.7 σ around water molecules (red spheres) and at 1 σ elsewhere.
11 fig S10. Cα-Cα difference distance matrix between A2A_S-SAD_1.9 and previously determined A2AAR structure (PDB: 4EIY). Residue numbers are shown on the top and right side of the matrix. Distance color scale (in Å) is given on the right side of the matrix.
12 Normalized B-factor difference B-factor, Ų A Residue number B Residue number fig. S11. B factor comparison between room temperature A2A_S-SAD_1.9 and previously determined cryocooled A2AAR structure (PDB: 4EIY). (A) Distribution of Cα atom B-factors for A2A_S-SAD_1.9 (red) and 4EIY (blue) vs. residue number. (B) Normalized Cα atom B-factor difference between A2A_S-SAD_1.9 and 4EIY structures.
13 fig. S12. Distribution of Cys and Met residues in human proteins. All human proteins (red), transmembrane proteins (green), and GPCRs (blue) correspond to subsets of 20194, 5181 and 825 protein entries in UniProt (Swiss-Prot, retrieved Jan 1st 2016), respectively. The shaded area corresponds to values between the S-SAD phasing cutoff described in the main text (12 sulfur atoms) and the value obtained for the A2AAR (24 sulfur atoms). Proteins with a higher fraction of Cys and Met residues than the S-SAD phasing cutoff (2.7%) comprise more than 88.5% of all, 92.4% of transmembrane, and 99.9% of all GPCR proteins.
14 table S1. Data collection statistics. Highest-resolution shell is shown in parentheses. Dataset A 2A_S-SAD A 2A _High-Res Wavelength (Å) Pulse duration, fs Flux, photons/pulse Max dose per crystal, MGy Space group C2221 C2221 Unit cell parameters a,b,c (Å) Number of collected images 7,324, ,961 Number of hits / indexed images Number of total / unique reflections 1,797,503 / 578, ,283 / 72,735 38,036,147 / 34,140 # 12,215,692 / 41,882 Resolution (Å) ( ) ( ) Mean I/σ(I) 20.3 (1.6) # 6.0 (0.6) Completeness (%) 100 (83.5) # 100 (100) Multiplicity 1022 (7) # 291 (62) Rsplit (%) 4.1 (75.1) # 10.1 (197) CC* (0.69) # (0.58) # considering Friedel pairs as individual reflections
15 table S2. Data refinement statistics. Highest-resolution shell is shown in parentheses. Structure A 2A S-SAD_1.9 A 2A MR_1.9 A 2A S-SAD_2.5 A 2A MR_2.5 Resolution (Å) No reflections / test set 41,828 / 1,988 41,828 / 1,988 18,567 / ,622 / 900 Rwork / Rfree / / / / Number of atoms All A2AAR BRIL ZM Na + ion Waters Lipids and other 3,632 2, ,636 2, ,508 2, ,484 2, Wilson B (Å 2 ) Mean overall B (Å 2 ) All A2AAR BRIL ZM Na + ion Waters Lipids and other R.m.s. deviations Bond lengths (Å) Bond angles ( ) Clash Score # Cβ outliers (%) # Rotamer outliers (%) # Ramanchandran plot statistics (%) # Favored regions Allowed regions Disallowed regions # As defined in MolProbity (44)
16 table S3. Comparison of interactions involving charged residues between PDB: 4EIY and A2A_S-SAD_1.9 structures. Interactions which were observed in the A2A_S-SAD_1.9 to be more/equally/less favorable are highlighted in green/gray/red, respectively. Interactions involving disordered residues are highlighted in dark gray. Residue 1 Residue 2 Distance, Å 4EIY Distance, Å A 2A_S-SAD_1.9 ΔB Residue 1, Å 2 (atom) ΔB Residue 2, Å 2 (atom) K150 D (NZ) 14.7 (OD1) E151 H (O) 15.7 (ND1) K153 D (NZ) 14.4 (OD2) E294 N (OE2) 18.5 (ND2) D101 R (OD2) 16.9 (NH2) D101 R (OD2) 20.6 (NE) R120 L (NH2) 31.5 (O) E169 H (OE1) 10.3 (NE2) E13 H (OE2) 12.6 (ND1) E13 H (OE1) 12.6 (ND1) R291 S (NE) 17.2 (OG) E151 N (OE1) 19.1 (ND2:A) R300 Q (NH1:B) 30.7 (OE1) table S4. Comparison of protein and data collection parameters for successful S-SAD phasing of XFEL data. Lysozyme (22) Thaumatin (23) A2AAR-BRIL Molecular weight (kda) Ordered Cys and Met residues 10 # Total residues % Cys and Met 7.8 # Crystal size (μm) Crystal solvent content (%) Space group P P C X-ray energy (kev) Minimum number of indexed patterns sufficient for indexing 150, , ,000 Protein used, mg # Anomalous signal from one chloride atom was used in addition to sulfurs.
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