5YLU

Crystal structure of the gastric proton pump complexed with vonoprazan


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5Y0B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529310% glycerol, 20% PEG2000MME, 0.4M CH3COONa, 3% methylpentanediol, 5mM beta-mercaptoethanol
Crystal Properties
Matthews coefficientSolvent content
4.2571.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.82α = 90
b = 104.82β = 90
c = 367.08γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS3 S 6M2017-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.848.1887.510.12010.0574811.045.25865240.6363630375
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)RedundancyNumber Unique Reflections (All)
12.82.938.171.6890.78731.545.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5Y0B2.7998896231948.17666671.3478261661651504261087.5114690590.2393182086540.2367149234570.28836007530343.7477478754
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d21.6974865055
f_angle_d1.31284041837
f_chiral_restr0.0803352081031
f_bond_d0.010924197444
f_plane_restr0.00782404207933
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9624
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms223

Software

Software
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing