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Mutant Imine Reductase IR007-143 from Amycolatopsis azurea, E120A, M197W, M206S, A213P, D238G, I240L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JIZ 6JIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M bistris, 0.1 M NaCl, 1.5 M ammonium sulfate, 6% 1,4-butanediol
Crystal Properties Matthews coefficient Solvent content 5.03 75.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.027 α = 90 b = 186.027 β = 90 c = 373.436 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 120 PIXEL DECTRIS EIGER2 XE 16M 2021-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 62.32 100 0.16 0.05 1 14.8 21.4 68344
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.76 100 1.23 0.38 0.86 2.7
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 6JIZ 2.7 62.32 64923 3394 99.95 0.18932 0.1882 0.2016 0.21087 0.2212 RANDOM 60.075
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] 0.61 0.31 0.61 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.477 r_dihedral_angle_3_deg 18.649 r_dihedral_angle_4_deg 18.116 r_long_range_B_other 11.044 r_long_range_B_refined 11.042 r_scangle_other 9.303 r_mcangle_it 8.385 r_mcangle_other 8.385 r_dihedral_angle_1_deg 6.777 r_scbond_it 6.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.477 r_dihedral_angle_3_deg 18.649 r_dihedral_angle_4_deg 18.116 r_long_range_B_other 11.044 r_long_range_B_refined 11.042 r_scangle_other 9.303 r_mcangle_it 8.385 r_mcangle_other 8.385 r_dihedral_angle_1_deg 6.777 r_scbond_it 6.596 r_scbond_other 6.563 r_mcbond_it 6.064 r_mcbond_other 6.041 r_angle_refined_deg 1.747 r_angle_other_deg 1.393 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8554 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 232
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing