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Crystal structure of the gastric proton pump complexed with SCH28080
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YLU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 10% glycerol, 20% PEG2000MME, 0.2M RbCl, 5% tert-butanol, 5mM beta-mercaptoethanol
Crystal Properties Matthews coefficient Solvent content 3.98 69.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.05 α = 90 b = 105.05 β = 90 c = 368.54 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 EIGER X 9M 2017-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 48.3 92.27 9.88 7.8 59284 73.9593491835
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 40.65 2.35 0.86 0.84 8.2
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 5YLU 2.79977781895 48.2956647824 1.34545459227 54741 2746 92.2637407089 0.242277654791 0.239649552158 0.2396 0.292091713448 0.2935 69.8135855892
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 21.222181132 f_angle_d 1.26110914127 f_chiral_restr 0.119492268459 f_bond_d 0.0101564555104 f_plane_restr 0.00797006218924
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9739 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 169
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing