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Imine Reductase from Myxococcus stipitatus V8 variant in complex with NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OCM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.1 M HEPES pH 7.0; 20% (w/v) PEG 6K; o.2 M ammonium choride
Crystal Properties Matthews coefficient Solvent content 2.77 55.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.412 α = 90 b = 199.412 β = 90 c = 97.94 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 120 PIXEL DECTRIS PILATUS3 6M 2018-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 2.78 48.97 100 0.17 0.05 1 16.1 20.4 55975 35
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 2.78 2.86 0.91 0.29 0.91 4
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 5OCM 2.78 47.94 53100 2844 99.97 0.1937 0.1918 0.1945 0.2279 0.2278 RANDOM 44.497
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] -0.34 -0.17 -0.34 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.694 r_dihedral_angle_4_deg 24.683 r_dihedral_angle_3_deg 19.844 r_dihedral_angle_1_deg 6.368 r_angle_refined_deg 1.553 r_angle_other_deg 1.332 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.694 r_dihedral_angle_4_deg 24.683 r_dihedral_angle_3_deg 19.844 r_dihedral_angle_1_deg 6.368 r_angle_refined_deg 1.553 r_angle_other_deg 1.332 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12822 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing