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Imine Reductase from Bacillus cereus in complex with NADH
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 291 PEG3350,magnesium diformate
Crystal Properties Matthews coefficient Solvent content 2.11 41.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.08 α = 90 b = 72.4 β = 90 c = 122.84 γ = 90
Symmetry Space Group P 21 21 21
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 Bruker PHOTON III 2023-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 0.979183
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.13 54.03 99.6 0.999 12.5 11.6 30625
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.19 0.832
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 2.13 54.03 29116 1451 99.55 0.21062 0.20746 0.2131 0.2738 0.2774 RANDOM 53.983
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] 0.53 4.33 -4.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.381 r_dihedral_angle_4_deg 21.684 r_dihedral_angle_3_deg 18.642 r_long_range_B_other 10.031 r_long_range_B_refined 10.029 r_scangle_other 7.899 r_mcangle_it 6.815 r_mcangle_other 6.814 r_dihedral_angle_1_deg 6.773 r_scbond_it 5.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.381 r_dihedral_angle_4_deg 21.684 r_dihedral_angle_3_deg 18.642 r_long_range_B_other 10.031 r_long_range_B_refined 10.029 r_scangle_other 7.899 r_mcangle_it 6.815 r_mcangle_other 6.814 r_dihedral_angle_1_deg 6.773 r_scbond_it 5.561 r_scbond_other 5.56 r_mcbond_it 5.1 r_mcbond_other 5.097 r_angle_refined_deg 1.666 r_angle_other_deg 1.342 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 4412 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing