5LBU

Structure of the human quinone reductase 2 (NQO2) in complex with to CL097


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BZS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M Tris HCl pH 8.5 2 M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.3146.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.694α = 90
b = 80.853β = 90
c = 106.016γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

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
11.6544.3990.0690.9989.423.459424
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)
11.651.71920.80.92.2

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 SYNTHESISTHROUGHOUT2BZS1.6544.356454296798.610.181540.180140.2083RANDOM26.614
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]
2.45-0.41-2.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.043
r_dihedral_angle_4_deg13.255
r_dihedral_angle_3_deg11.039
r_dihedral_angle_1_deg6.13
r_long_range_B_refined4.734
r_long_range_B_other4.734
r_scangle_other2.647
r_mcangle_other2.14
r_mcangle_it2.139
r_scbond_it1.613
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.043
r_dihedral_angle_4_deg13.255
r_dihedral_angle_3_deg11.039
r_dihedral_angle_1_deg6.13
r_long_range_B_refined4.734
r_long_range_B_other4.734
r_scangle_other2.647
r_mcangle_other2.14
r_mcangle_it2.139
r_scbond_it1.613
r_scbond_other1.612
r_angle_refined_deg1.412
r_mcbond_it1.314
r_mcbond_other1.3
r_angle_other_deg0.89
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3612
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms205

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing