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Azoreductase (AzoRo) from Rhodococcus opacus 1CP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other homology model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 16-20% of isopropanol, 12-16% PEG4000 and 0.1M of sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.55 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.652 α = 90 b = 140.652 β = 90 c = 40.568 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2019-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.2 70.43 99.87 0.133 0.148 0.063 0.997 10.7 5.6 23710 39.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 1.654 1.84 0.795 0.53 5.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE homology model 2.2 70.33 23709 1221 99.903 0.218 0.2161 0.2165 0.2611 0.2611 53.42
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] -0.118 -0.059 -0.118 0.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.203 r_dihedral_angle_4_deg 18.087 r_dihedral_angle_3_deg 15.853 r_dihedral_angle_1_deg 6.58 r_lrange_it 5.53 r_lrange_other 5.516 r_scangle_it 2.772 r_scangle_other 2.772 r_mcangle_other 2.31 r_mcangle_it 2.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.203 r_dihedral_angle_4_deg 18.087 r_dihedral_angle_3_deg 15.853 r_dihedral_angle_1_deg 6.58 r_lrange_it 5.53 r_lrange_other 5.516 r_scangle_it 2.772 r_scangle_other 2.772 r_mcangle_other 2.31 r_mcangle_it 2.309 r_scbond_it 1.746 r_scbond_other 1.746 r_angle_refined_deg 1.731 r_mcbond_it 1.47 r_mcbond_other 1.468 r_angle_other_deg 1.335 r_nbd_refined 0.186 r_symmetry_nbd_refined 0.16 r_nbd_other 0.157 r_symmetry_nbd_other 0.154 r_nbtor_refined 0.149 r_ncsr_local_group_1 0.141 r_symmetry_xyhbond_nbd_refined 0.136 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3119 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing