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Horse liver alcohol dehydrogenase in complex with NADH and N-cylcohexyl formamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DWV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 50 mM Tris-HCl buffer at pH 8.2, 18% (v/v) PEG400
Crystal Properties Matthews coefficient Solvent content 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.142 α = 92.41 b = 50.979 β = 103.03 c = 92.864 γ = 108.94
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 2020-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.43 37.94 87.2 0.06 0.064 0.023 0.999 19.7 7.8 119395
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.45 85.5 1.671 1.795 0.651 0.754 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 4DWV 1.43 37.94 1.96 117400 5867 85.81 0.1905 0.1895 0.204 0.2082 0.2111 28.5543
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 11.69 f_angle_d 2.667 f_chiral_restr 0.254 f_bond_d 0.021 f_plane_restr 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5570 Nucleic Acid Atoms Solvent Atoms 777 Heterogen Atoms 110
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing