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Imine reductase from Aspergillus oryzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 pH 7
Crystal Properties Matthews coefficient Solvent content 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.27 α = 90 b = 92.44 β = 100.33 c = 84.51 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 120 PIXEL DECTRIS PILATUS 6M 2016-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.82 61.82 99.6 0.04 15.9 2 53033 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 1.82 1.87 99.7 0.77 1.7 2.1
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 5A9T 1.82 61.82 50474 2539 99.59 0.18703 0.18517 0.1929 0.22514 0.2303 RANDOM 38.908
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] 0.74 -0.46 -0.31 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.401 r_dihedral_angle_4_deg 30.194 r_dihedral_angle_3_deg 15.609 r_dihedral_angle_1_deg 5.264 r_scbond_it 4.854 r_mcangle_it 4.768 r_mcbond_it 3.619 r_mcbond_other 3.616 r_angle_refined_deg 2.007 r_angle_other_deg 1.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.401 r_dihedral_angle_4_deg 30.194 r_dihedral_angle_3_deg 15.609 r_dihedral_angle_1_deg 5.264 r_scbond_it 4.854 r_mcangle_it 4.768 r_mcbond_it 3.619 r_mcbond_other 3.616 r_angle_refined_deg 2.007 r_angle_other_deg 1.457 r_chiral_restr 0.133 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 4131 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing