7W48

Crystal structure of the gastric proton pump complexed with PF-03716556


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529310% glycerol, 0.2 M RbCl, 20% PEG2000MME, 3% tert-BuOH, 5 mM beta-MeSH
Crystal Properties
Matthews coefficientSolvent content
3.9668.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.75α = 90
b = 104.75β = 90
c = 368.79γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77PIXELDECTRIS EIGER X 16M2018-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
13.548.1875.310.9985.556.73041783.51
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.6260.318

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-VALUE5ylv3.548.181.3123045120875.360.25510.25230.306584.28
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_d15.6543
f_angle_d0.9019
f_chiral_restr0.0612
f_plane_restr0.0068
f_bond_d0.0042
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9739
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms177

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing