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Imine Reductase from Aspergillus terreus in complex with NADPH4 and dibenz[c,e]azepine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M Bis-tris pH 5.5.
25% w/v PEG 3350
0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.329 α = 90 b = 61.128 β = 90 c = 167.811 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS 6M-F 2017-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.928190 Diamond I04-1
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 1.56 41.95 100 0.04 0.02 1 23.5 8.1 39537
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 1.56 1.59 100 0.75 0.41 0.88 2.3 8.4
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 5A9S 1.56 41.95 37441 2043 99.97 0.23724 0.23508 0.2453 0.2778 0.2894 RANDOM 34.331
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] -0.08 2.17 -2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.825 r_dihedral_angle_3_deg 16.281 r_dihedral_angle_4_deg 15.864 r_long_range_B_other 6.699 r_long_range_B_refined 6.698 r_dihedral_angle_1_deg 6.348 r_scangle_other 5.014 r_mcangle_it 4.64 r_mcangle_other 4.638 r_scbond_it 3.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.825 r_dihedral_angle_3_deg 16.281 r_dihedral_angle_4_deg 15.864 r_long_range_B_other 6.699 r_long_range_B_refined 6.698 r_dihedral_angle_1_deg 6.348 r_scangle_other 5.014 r_mcangle_it 4.64 r_mcangle_other 4.638 r_scbond_it 3.784 r_scbond_other 3.774 r_mcbond_it 3.598 r_mcbond_other 3.594 r_angle_refined_deg 2.173 r_angle_other_deg 1.163 r_chiral_restr 0.134 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 2004 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing