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Imine Reductase IR007 from Amycolatopsis azurea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JIZ 6JIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 298 0.49 M sodium phosphate; o.91 M potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.65 53.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.487 α = 90 b = 142.332 β = 90 c = 159.931 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 120 PIXEL DECTRIS EIGER2 X 16M 2021-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.72 54.1 100 0.31 0.12 0.99 6.6 13.6 36218 19
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 2.72 2.84 0.98 0.38 0.95 2.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6JIZ 2.72 54.1 34255 1812 99.74 0.24828 0.24688 0.27328 0.2566 RANDOM 34.189
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] 0.11 7.44 -7.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.191 r_dihedral_angle_3_deg 19.074 r_dihedral_angle_4_deg 18.523 r_dihedral_angle_1_deg 6.622 r_long_range_B_refined 6.616 r_long_range_B_other 6.599 r_mcangle_it 3.928 r_mcangle_other 3.928 r_scangle_other 3.703 r_mcbond_it 2.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.191 r_dihedral_angle_3_deg 19.074 r_dihedral_angle_4_deg 18.523 r_dihedral_angle_1_deg 6.622 r_long_range_B_refined 6.616 r_long_range_B_other 6.599 r_mcangle_it 3.928 r_mcangle_other 3.928 r_scangle_other 3.703 r_mcbond_it 2.475 r_mcbond_other 2.475 r_scbond_it 2.28 r_scbond_other 2.279 r_angle_refined_deg 1.446 r_angle_other_deg 1.25 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 8539 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing