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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)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V4B PDB ENTRY 1V4B
Crystallization Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.204 α = 90 b = 92.204 β = 90 c = 51.741 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 4 2002-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.0000 Photon Factory BL-18B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.4 64.55 42307
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1V4B 1.4 34.3 40396 2155 95.95 0.18586 0.18403 0.1935 0.21982 0.2286 RANDOM 13.436
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] 0.4 0.4 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.055 r_dihedral_angle_4_deg 23.574 r_dihedral_angle_3_deg 12.861 r_dihedral_angle_1_deg 5.892 r_scangle_it 5.462 r_scbond_it 4.608 r_angle_refined_deg 3.739 r_mcangle_it 2.742 r_mcbond_it 2.403 r_angle_other_deg 1.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.055 r_dihedral_angle_4_deg 23.574 r_dihedral_angle_3_deg 12.861 r_dihedral_angle_1_deg 5.892 r_scangle_it 5.462 r_scbond_it 4.608 r_angle_refined_deg 3.739 r_mcangle_it 2.742 r_mcbond_it 2.403 r_angle_other_deg 1.507 r_mcbond_other 0.622 r_nbd_refined 0.236 r_symmetry_vdw_other 0.233 r_nbd_other 0.221 r_chiral_restr 0.218 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.16 r_symmetry_vdw_refined 0.121 r_nbtor_other 0.1 r_bond_refined_d 0.046 r_gen_planes_refined 0.018 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1476 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement