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Crystal Structure of Glycerol Dehydrogenase in the absence of NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM sodium citrate (pH 5.6), 500 mM ammonium sulfate, and 1 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 5.97 79.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.47 α = 90 b = 161.47 β = 90 c = 291.907 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS3 6M 2019-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.9794 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.9 49.24 99.6 0.99 6.8 8.7 86081
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 0.322
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 5zxl 2.9 49.24 1.33 85847 4362 99.83 0.1937 0.1923 0.1956 0.2199 0.223
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 6.929 f_angle_d 0.914 f_chiral_restr 0.053 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10844 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing