4CET

Crystal structure of the complex of the P187S variant of human NAD(P) H:quinone oxidoreductase with dicoumarol at 2.2 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QBGPDB ENTRY 1QBG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5PROTEIN WAS CRYSTALLIZED FROM 0.005 M CO(II)CL-HEXAHYDRATE, 0.005 M NI(II)CL-HEXAHYDRATE, 0.005 M CDCL-HYDRATE, 0.005 M MGCL-HEAXHYDRATE, 0.1 M HEPES PH 7.5, 12 % PEG-3350 (W/V)
Crystal Properties
Matthews coefficientSolvent content
1.6726.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.05α = 90
b = 51.05β = 90
c = 169.04γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS2012-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2RELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.233.899.80.1218.311.9121273.226.84
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.26980.663.29

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 1QBG2.233.1971.341206557699.770.1780.17550.223934.2
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_d15.626
f_angle_d0.895
f_chiral_restr0.06
f_bond_d0.004
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1768
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms78

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing