1ZX1

Human quinone oxidoreductase 2 (NQO2) in complex with the cytostatic prodrug CB1954


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QR2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7294Hepes, ammonium sulphate, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.328α = 90
b = 84.341β = 90
c = 106.579γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2005-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.90010SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.15097.40.128112918729187
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1882.80.4112

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1QR22.16502563725637136596.760.175910.175910.174180.20656RANDOM39.515
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]
-0.010.08-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.628
r_dihedral_angle_4_deg25.192
r_dihedral_angle_3_deg15.071
r_dihedral_angle_1_deg6.122
r_scangle_it3.357
r_scbond_it2.093
r_angle_refined_deg1.516
r_mcangle_it1.279
r_mcbond_it0.808
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.628
r_dihedral_angle_4_deg25.192
r_dihedral_angle_3_deg15.071
r_dihedral_angle_1_deg6.122
r_scangle_it3.357
r_scbond_it2.093
r_angle_refined_deg1.516
r_mcangle_it1.279
r_mcbond_it0.808
r_nbtor_refined0.309
r_symmetry_vdw_refined0.246
r_symmetry_hbond_refined0.205
r_nbd_refined0.197
r_xyhbond_nbd_refined0.149
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_metal_ion_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3565
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing