5LBW

Structure of the human quinone reductase 2 (NQO2) in complex with volitinib


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293200 mM sodium sulphate, 2.2 M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.3246.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.398α = 90
b = 81.372β = 90
c = 106.403γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2015-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.979SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.944.5900.110.9967.494.736213
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)
11.91.97930.971.34

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5LBU1.944.534410180390.50.254040.253170.2705RANDOM42.198
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]
8.01-2.77-5.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.722
r_dihedral_angle_4_deg13.944
r_dihedral_angle_3_deg12.839
r_dihedral_angle_1_deg6.189
r_long_range_B_refined2.888
r_long_range_B_other2.887
r_angle_refined_deg1.317
r_angle_other_deg0.896
r_scangle_other0.481
r_mcangle_it0.478
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.722
r_dihedral_angle_4_deg13.944
r_dihedral_angle_3_deg12.839
r_dihedral_angle_1_deg6.189
r_long_range_B_refined2.888
r_long_range_B_other2.887
r_angle_refined_deg1.317
r_angle_other_deg0.896
r_scangle_other0.481
r_mcangle_it0.478
r_mcangle_other0.478
r_scbond_it0.278
r_scbond_other0.278
r_mcbond_it0.274
r_mcbond_other0.273
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms3608
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing