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Imine reductase from Aspergillus oryzae in complex with NADP(H) and (R)-rasagiline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A9T PDB ENTRY 5A9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 pH 7
Crystal Properties Matthews coefficient Solvent content 2.94 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.822 α = 108.75 b = 80.255 β = 108.78 c = 123.895 γ = 90.05
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 2015-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.35 75.48 97.4 0.2 2.9 1.8 111053 2
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 2.35 2.39 97.1 0.55 1.2 1.8
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 PDB ENTRY 5A9T 2.35 110.32 105360 5656 97.35 0.20563 0.20431 0.2077 0.22902 0.2294 RANDOM 38.32
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] 1.13 -0.32 -0.42 0.69 -0.25 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.514 r_dihedral_angle_4_deg 21.718 r_dihedral_angle_3_deg 15.965 r_dihedral_angle_1_deg 5.436 r_mcangle_it 3.576 r_scbond_it 2.77 r_mcbond_it 2.353 r_mcbond_other 2.352 r_angle_refined_deg 1.701 r_angle_other_deg 1.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.514 r_dihedral_angle_4_deg 21.718 r_dihedral_angle_3_deg 15.965 r_dihedral_angle_1_deg 5.436 r_mcangle_it 3.576 r_scbond_it 2.77 r_mcbond_it 2.353 r_mcbond_other 2.352 r_angle_refined_deg 1.701 r_angle_other_deg 1.349 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16864 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 488
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing