2Z9C

The crystal structure of AzoR (azoreductase) from Escherichia coli: AzoR in complex with dicoumarol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V4BPDB ID 1V4B

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.8857.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.5α = 90
b = 95.5β = 90
c = 54.497γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 42003-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A0.9780Photon FactoryBL-6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.319.899493

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 ID 1V4B2.319.88902144781.140.17840.176340.21955RANDOM31.175
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]
-1.47-1.472.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.542
r_dihedral_angle_4_deg17.896
r_dihedral_angle_3_deg13.197
r_dihedral_angle_1_deg5.569
r_scangle_it1.763
r_scbond_it1.281
r_angle_refined_deg1.205
r_mcangle_it0.989
r_angle_other_deg0.906
r_mcbond_it0.899
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.542
r_dihedral_angle_4_deg17.896
r_dihedral_angle_3_deg13.197
r_dihedral_angle_1_deg5.569
r_scangle_it1.763
r_scbond_it1.281
r_angle_refined_deg1.205
r_mcangle_it0.989
r_angle_other_deg0.906
r_mcbond_it0.899
r_nbd_refined0.189
r_nbd_other0.185
r_nbtor_refined0.177
r_symmetry_vdw_other0.164
r_xyhbond_nbd_refined0.119
r_mcbond_other0.102
r_symmetry_hbond_refined0.098
r_symmetry_vdw_refined0.083
r_nbtor_other0.08
r_chiral_restr0.074
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1499
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement