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NADPH and 1-benzyl-4-methylpiperidin-3-one complex structure of Imine Reductase Mutant(M6) from Pochonia chlamydosporia 170
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, SITTING DROP 298 PEG3350, magnesium chloride, Tris-Hcl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.13 42.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.85 α = 90 b = 114.45 β = 99.05 c = 62.61 γ = 90
Symmetry Space Group P 1 21 1
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 2023-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979183 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.13 42.03 78.3 0.043 7.9 5.8 865651
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.16 0.297 1.8
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 1.13 42.03 141826 7541 78.32 0.15501 0.1539 0.1631 0.17557 0.1822 RANDOM 15.347
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] 1.08 0.2 -0.51 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.883 r_dihedral_angle_4_deg 16.609 r_dihedral_angle_3_deg 11.545 r_dihedral_angle_1_deg 5.341 r_long_range_B_refined 5.234 r_long_range_B_other 5.059 r_scangle_other 4.098 r_scbond_it 2.785 r_scbond_other 2.785 r_angle_refined_deg 2.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.883 r_dihedral_angle_4_deg 16.609 r_dihedral_angle_3_deg 11.545 r_dihedral_angle_1_deg 5.341 r_long_range_B_refined 5.234 r_long_range_B_other 5.059 r_scangle_other 4.098 r_scbond_it 2.785 r_scbond_other 2.785 r_angle_refined_deg 2.001 r_mcangle_it 1.762 r_mcangle_other 1.762 r_angle_other_deg 1.618 r_mcbond_it 1.264 r_mcbond_other 1.264 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 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 4206 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing