8OK0

Crystal structure of human NQO1 in complex with the inhibitor PMSF


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A4K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291.150.1 M Tris pH 8.5, 0.2 M Sodium Acetate, 20% polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.3247.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.172α = 90
b = 58.928β = 98.93
c = 189.161γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.98ALBAXALOC

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
11.649.5299.50.99911.76.6135910
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)
11.61.6494.30.076

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.649.471359101512998.130.211780.207880.24654RANDOM32.967
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
r_dihedral_angle_3_deg14.267
r_long_range_B_other8.869
r_long_range_B_refined8.839
r_dihedral_angle_1_deg6.498
r_dihedral_angle_2_deg5.995
r_scangle_other5.779
r_mcangle_it4.167
r_mcangle_other4.167
r_scbond_it3.663
r_scbond_other3.663
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.267
r_long_range_B_other8.869
r_long_range_B_refined8.839
r_dihedral_angle_1_deg6.498
r_dihedral_angle_2_deg5.995
r_scangle_other5.779
r_mcangle_it4.167
r_mcangle_other4.167
r_scbond_it3.663
r_scbond_other3.663
r_mcbond_it2.932
r_mcbond_other2.932
r_angle_refined_deg1.42
r_angle_other_deg0.53
r_chiral_restr0.077
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d0.003
r_gen_planes_other0.002
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8913
Nucleic Acid Atoms
Solvent Atoms1016
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing