2BZS

Binding of anti-cancer prodrug CB1954 to the activating enzyme NQO2 revealed by the crystal structure of their complex.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QR2PDB ENTRY 1QR2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
171.66M AMM. SULF IN 100MM NA-HEPES PH 7 AND 12MICROM FAD, 1MM DTT
Crystal Properties
Matthews coefficientSolvent content
2.248

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.83α = 90
b = 106.11β = 90
c = 61.65γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IVVARIMAX HF2005-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
123099.40.0813.96.43638230.54
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)
122.1196.30.434.5

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QR223034512181399.40.1960.1930.247RANDOM32.47
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]
3.08-2.89-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.426
r_dihedral_angle_4_deg23.974
r_dihedral_angle_3_deg14.808
r_dihedral_angle_1_deg7.386
r_scangle_it4.066
r_scbond_it2.606
r_angle_refined_deg1.865
r_mcangle_it1.782
r_mcbond_it1.134
r_symmetry_hbond_refined0.698
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.426
r_dihedral_angle_4_deg23.974
r_dihedral_angle_3_deg14.808
r_dihedral_angle_1_deg7.386
r_scangle_it4.066
r_scbond_it2.606
r_angle_refined_deg1.865
r_mcangle_it1.782
r_mcbond_it1.134
r_symmetry_hbond_refined0.698
r_nbtor_refined0.314
r_symmetry_vdw_refined0.309
r_nbd_refined0.219
r_xyhbond_nbd_refined0.212
r_chiral_restr0.119
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3648
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling