5LBT

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


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
2.3146.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.689α = 90
b = 80.925β = 90
c = 106.198γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-04-08MSINGLE 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
11.7544.4930.1240.9956.014.649249
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)
11.751.81751.60.054.7

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 SYNTHESISTHROUGHOUT2BZS1.7544.445013237293.270.199090.197650.22652RANDOM27.413
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]
1.770.03-1.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.75
r_dihedral_angle_4_deg16.838
r_dihedral_angle_3_deg11.868
r_dihedral_angle_1_deg6.321
r_long_range_B_refined4.587
r_long_range_B_other4.544
r_angle_refined_deg1.716
r_scangle_other1.256
r_mcangle_it1.046
r_mcangle_other1.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.75
r_dihedral_angle_4_deg16.838
r_dihedral_angle_3_deg11.868
r_dihedral_angle_1_deg6.321
r_long_range_B_refined4.587
r_long_range_B_other4.544
r_angle_refined_deg1.716
r_scangle_other1.256
r_mcangle_it1.046
r_mcangle_other1.046
r_angle_other_deg0.975
r_scbond_it0.85
r_scbond_other0.769
r_mcbond_it0.623
r_mcbond_other0.619
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.008
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 Atoms3599
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms195

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing