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Crystal structure of the gastric proton pump complexed with vonoprazan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Y0B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 10% glycerol, 20% PEG2000MME, 0.4M CH3COONa, 3% methylpentanediol, 5mM beta-mercaptoethanol
Crystal Properties Matthews coefficient Solvent content 4.25 71.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.82 α = 90 b = 104.82 β = 90 c = 367.08 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 S 6M 2017-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 48.18 87.51 0.1201 0.05748 11.04 5.2 58652 40.6363630375
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 38.17 1.689 0.7873 1.54 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5Y0B 2.79988962319 48.1766667 1.34782616616 51504 2610 87.511469059 0.239318208654 0.236714923457 0.2391 0.288360075303 0.291 43.7477478754
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.6974865055 f_angle_d 1.31284041837 f_chiral_restr 0.0803352081031 f_bond_d 0.010924197444 f_plane_restr 0.00782404207933
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9624 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 223
Software Software Software Name Purpose phenix.refine refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing