6C45

Crystal structure of human inorganic pyrophosphatase in the P212121 space group


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729320% PEG3350, 100 mM Bis-Tris, pH 7.5, 200 mM potassium bromide, 10% v/v glycerol
Crystal Properties
Matthews coefficientSolvent content
2.8556.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.25α = 90
b = 136.94β = 90
c = 216.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2017-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0,987APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
12.38884.93199.90.1190.1360.0648.24.5604976049739.18
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.392.5299.50.6870.6870.8010.40114.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.38865.281.2360334199899.810.1950.1930.251125.02
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_d14.093
f_angle_d1.248
f_chiral_restr0.084
f_bond_d0.008
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9031
Nucleic Acid Atoms
Solvent Atoms526
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing