2Z98

The crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in tetragonal crystals (The resolution has improved from 1.8 (1v4b) to 1.4 angstrom)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.5551.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.204α = 90
b = 92.204β = 90
c = 51.741γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 42002-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-18B1.0000Photon FactoryBL-18B

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
11.464.5542307

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 1V4B1.434.340396215595.950.185860.184030.21982RANDOM13.436
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]
0.40.4-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.055
r_dihedral_angle_4_deg23.574
r_dihedral_angle_3_deg12.861
r_dihedral_angle_1_deg5.892
r_scangle_it5.462
r_scbond_it4.608
r_angle_refined_deg3.739
r_mcangle_it2.742
r_mcbond_it2.403
r_angle_other_deg1.507
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.055
r_dihedral_angle_4_deg23.574
r_dihedral_angle_3_deg12.861
r_dihedral_angle_1_deg5.892
r_scangle_it5.462
r_scbond_it4.608
r_angle_refined_deg3.739
r_mcangle_it2.742
r_mcbond_it2.403
r_angle_other_deg1.507
r_mcbond_other0.622
r_nbd_refined0.236
r_symmetry_vdw_other0.233
r_nbd_other0.221
r_chiral_restr0.218
r_nbtor_refined0.19
r_xyhbond_nbd_refined0.163
r_symmetry_hbond_refined0.16
r_symmetry_vdw_refined0.121
r_nbtor_other0.1
r_bond_refined_d0.046
r_gen_planes_refined0.018
r_bond_other_d0.002
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 Atoms1476
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement