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Imine Reductase from Streptosporangium roseum in complex with NADP+ and 2,2,2-trifluoroacetophenone hydrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M Tris-HCl pH 8.0; 20% PEG 6000; 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.49 50.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.811 α = 90 b = 152.434 β = 90 c = 251.598 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 2017-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.81 125.8 100 0.11 0.06 13.7 8.2 161732
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.84 0.85 0.48
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 3ZHB 1.81 125.8 153606 8058 99.98 0.16947 0.16812 0.1792 0.19573 0.2054 RANDOM 19.477
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] -0.63 -0.88 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.15 r_dihedral_angle_4_deg 19.421 r_dihedral_angle_3_deg 12.845 r_dihedral_angle_1_deg 4.903 r_long_range_B_refined 4.825 r_long_range_B_other 4.825 r_scangle_other 4.167 r_scbond_it 2.871 r_scbond_other 2.871 r_mcangle_it 2.411
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.15 r_dihedral_angle_4_deg 19.421 r_dihedral_angle_3_deg 12.845 r_dihedral_angle_1_deg 4.903 r_long_range_B_refined 4.825 r_long_range_B_other 4.825 r_scangle_other 4.167 r_scbond_it 2.871 r_scbond_other 2.871 r_mcangle_it 2.411 r_mcangle_other 2.411 r_angle_refined_deg 1.828 r_mcbond_it 1.812 r_mcbond_other 1.811 r_angle_other_deg 1.08 r_chiral_restr 0.147 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 12443 Nucleic Acid Atoms Solvent Atoms 1139 Heterogen Atoms 373
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing