5LBZ

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


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
2.4149.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.454α = 90
b = 79.22β = 90
c = 106.23γ = 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 X06SA0.9785SLSX06SA

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
11.448.6950.0450.99921.114.597699
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)
11.41.45910.3295.34.4

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 SYNTHESISTHROUGHOUT5LBU1.448.693339491394.820.110050.108960.131RANDOM14.062
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]
0.440.25-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.757
r_sphericity_free29.752
r_dihedral_angle_4_deg19.468
r_sphericity_bonded13.608
r_dihedral_angle_3_deg11.382
r_rigid_bond_restr7.698
r_dihedral_angle_1_deg5.759
r_scangle_other4.833
r_scbond_it4.488
r_scbond_other4.443
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.757
r_sphericity_free29.752
r_dihedral_angle_4_deg19.468
r_sphericity_bonded13.608
r_dihedral_angle_3_deg11.382
r_rigid_bond_restr7.698
r_dihedral_angle_1_deg5.759
r_scangle_other4.833
r_scbond_it4.488
r_scbond_other4.443
r_long_range_B_refined4.344
r_long_range_B_other4.098
r_mcangle_other1.917
r_mcangle_it1.916
r_mcbond_it1.633
r_angle_refined_deg1.609
r_mcbond_other1.59
r_angle_other_deg1.204
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.007
r_bond_other_d0.004
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3604
Nucleic Acid Atoms
Solvent Atoms427
Heterogen Atoms198

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing