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The crystal structure of AzoR (azoreductase) from Escherichia coli: AzoR in complex with dicoumarol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V4B PDB ID 1V4B
Crystallization Crystal Properties Matthews coefficient Solvent content 2.88 57.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.5 α = 90 b = 95.5 β = 90 c = 54.497 γ = 90
Symmetry Space Group P 4 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 2003-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.9780 Photon Factory BL-6A
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 2.3 19.89 9493
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 ID 1V4B 2.3 19.88 9021 447 81.14 0.1784 0.17634 0.1852 0.21955 0.2269 RANDOM 31.175
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 -1.47 2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.542 r_dihedral_angle_4_deg 17.896 r_dihedral_angle_3_deg 13.197 r_dihedral_angle_1_deg 5.569 r_scangle_it 1.763 r_scbond_it 1.281 r_angle_refined_deg 1.205 r_mcangle_it 0.989 r_angle_other_deg 0.906 r_mcbond_it 0.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.542 r_dihedral_angle_4_deg 17.896 r_dihedral_angle_3_deg 13.197 r_dihedral_angle_1_deg 5.569 r_scangle_it 1.763 r_scbond_it 1.281 r_angle_refined_deg 1.205 r_mcangle_it 0.989 r_angle_other_deg 0.906 r_mcbond_it 0.899 r_nbd_refined 0.189 r_nbd_other 0.185 r_nbtor_refined 0.177 r_symmetry_vdw_other 0.164 r_xyhbond_nbd_refined 0.119 r_mcbond_other 0.102 r_symmetry_hbond_refined 0.098 r_symmetry_vdw_refined 0.083 r_nbtor_other 0.08 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 1499 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement