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Crystal Structure of Imine Reductase from Paenibacillus mucilaginosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D3F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2.0 M Ammonium sulfate, 0.1 M Sodium acetate/Hydrochloric acid pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.4 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.771 α = 90 b = 133.771 β = 90 c = 62.23 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2021-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9792 SSRF BL18U1
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 2.5 50 99.3 0.15 0.051 0.997 17.3 10.18 42733 28.78
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 2.5 2.54 100 0.904 0.281 0.89 4.9 10.99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 28.21 1.35 42074 2871 97.82 0.2095 0.2072 0.2078 0.2403 0.2414 43.7
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.6535 f_angle_d 1.0667 f_chiral_restr 0.0578 f_bond_d 0.0086 f_plane_restr 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4337 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling MOLREP phasing