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Structure of Imine Reductase 361 from Micromonospora sp. mutant M125W/I127F/L179V/H250L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OSN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 2M ammonium sulfate in bis-Tris buffer pH 6.5 with 2 mM NADP
Crystal Properties Matthews coefficient Solvent content 4.24 71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.268 α = 90 b = 184.268 β = 90 c = 184.268 γ = 90
Symmetry Space Group I 21 3
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 2024-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 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 2.77 130.3 93.7 0.1 0.02 1 37.6 40.4 15775 115
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 2.77 3.34 2.64 0.42 0.78 1.7
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 2.77 130.3 15067 708 59.57 0.22936 0.22578 0.233 0.30371 0.3056 RANDOM 102.514
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]
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 23.074 r_long_range_B_refined 23.067 r_dihedral_angle_3_deg 19.693 r_scangle_other 18.92 r_mcangle_it 17.802 r_mcangle_other 17.8 r_scbond_it 12.274 r_scbond_other 12.248 r_mcbond_it 11.743 r_mcbond_other 11.74
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 23.074 r_long_range_B_refined 23.067 r_dihedral_angle_3_deg 19.693 r_scangle_other 18.92 r_mcangle_it 17.802 r_mcangle_other 17.8 r_scbond_it 12.274 r_scbond_other 12.248 r_mcbond_it 11.743 r_mcbond_other 11.74 r_dihedral_angle_1_deg 8.058 r_dihedral_angle_2_deg 7.418 r_angle_refined_deg 1.502 r_angle_other_deg 0.536 r_chiral_restr 0.066 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3785 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing