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Imine Reductase from Rhodococcus erythropolis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M bis Tris propane pH 5.5; 0.2 M MgCl2; 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.66 α = 90 b = 80.66 β = 90 c = 82.78 γ = 120
Symmetry Space Group P 32 2 1
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 2024-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97627 Diamond I03
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 2.38 53.44 100 0.14 0.03 1 8.6 19.8 12900 47
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 2.38 2.47 0.98 0.22 0.96 0.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.38 53.44 12169 705 99.96 0.22179 0.21756 0.2286 0.29968 0.3031 RANDOM 67.858
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] 3.15 1.58 3.15 -10.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.865 r_long_range_B_refined 11.776 r_long_range_B_other 11.774 r_scangle_other 9.3 r_mcangle_it 9.095 r_mcangle_other 9.092 r_dihedral_angle_2_deg 8.901 r_dihedral_angle_1_deg 7.418 r_mcbond_it 6.121 r_mcbond_other 6.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.865 r_long_range_B_refined 11.776 r_long_range_B_other 11.774 r_scangle_other 9.3 r_mcangle_it 9.095 r_mcangle_other 9.092 r_dihedral_angle_2_deg 8.901 r_dihedral_angle_1_deg 7.418 r_mcbond_it 6.121 r_mcbond_other 6.12 r_scbond_it 6.033 r_scbond_other 6.03 r_angle_refined_deg 1.443 r_angle_other_deg 0.52 r_chiral_restr 0.071 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2052 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing