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Cd-substituted Horse Liver Alcohol Dehydrogenase in Complex with NADH and N-Cyclohexylformamide
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 PEG400(10%-25%), 2mM NADH, 10mM N-cyclohexylformamide in Tris buffer at pH 8.20
Crystal Properties Matthews coefficient Solvent content 2.24 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.206 α = 92.39 b = 50.807 β = 102.93 c = 92.903 γ = 109.33
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 EIGER X 16M 2021-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.979 SSRL BL12-1
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 1.33 38.02 88.5 0.071 0.076 0.027 0.999 16.1 7.7 150446
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 1.33 1.35 83.4 1.035 1.113 0.406 0.828 7.2
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 1.33 38.02 1.96 150245 7516 88.38 0.139 0.1376 0.1389 0.165 0.1661 19.0438
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5570 Nucleic Acid Atoms Solvent Atoms 1086 Heterogen Atoms 110
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing