2Z9B

The crystal structure of AzoR (azoreductase) from Escherichia coli: Reduced AzoR in tetragonal crystals


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.5351.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.882α = 90
b = 91.882β = 90
c = 51.623γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 42002-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0000Photon 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
11.764.9624003

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 1V4B1.727.522745122796.420.186340.184760.21596RANDOM15.127
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]
0.430.43-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.024
r_dihedral_angle_4_deg13.404
r_dihedral_angle_3_deg11.674
r_dihedral_angle_1_deg5.363
r_scangle_it3.569
r_scbond_it2.827
r_mcangle_it1.615
r_angle_refined_deg1.613
r_mcbond_it1.392
r_angle_other_deg0.956
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.024
r_dihedral_angle_4_deg13.404
r_dihedral_angle_3_deg11.674
r_dihedral_angle_1_deg5.363
r_scangle_it3.569
r_scbond_it2.827
r_mcangle_it1.615
r_angle_refined_deg1.613
r_mcbond_it1.392
r_angle_other_deg0.956
r_symmetry_hbond_refined0.318
r_mcbond_other0.292
r_symmetry_vdw_other0.213
r_nbd_refined0.206
r_nbd_other0.199
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.165
r_symmetry_vdw_refined0.156
r_chiral_restr0.093
r_nbtor_other0.087
r_bond_refined_d0.017
r_bond_other_d0.009
r_gen_planes_refined0.007
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 Atoms1468
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement