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Crystal structure of glycerol dehydrogenase (NP_348253.1) from Clostridium acetobutylicum at 2.37 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 NANODROP, 0.2M NaCl, 20.0% PEG 3000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.74 α = 90 b = 125.81 β = 102.33 c = 133.23 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2007-10-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.91840, 0.97953, 0.97939 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.37 28.94 96.9 0.05 8.2 66387 -3 53.802
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.37 2.45 91.4 0.401 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.37 28.94 66387 3364 98.54 0.189 0.188 0.1896 0.214 0.2143 RANDOM 40.094
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] -0.46 -0.55 -0.79 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.026 r_dihedral_angle_4_deg 17.442 r_dihedral_angle_3_deg 15.189 r_scangle_it 5.817 r_dihedral_angle_1_deg 4.249 r_scbond_it 3.719 r_mcangle_it 1.979 r_angle_refined_deg 1.33 r_angle_other_deg 1.256 r_mcbond_it 0.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.026 r_dihedral_angle_4_deg 17.442 r_dihedral_angle_3_deg 15.189 r_scangle_it 5.817 r_dihedral_angle_1_deg 4.249 r_scbond_it 3.719 r_mcangle_it 1.979 r_angle_refined_deg 1.33 r_angle_other_deg 1.256 r_mcbond_it 0.987 r_mcbond_other 0.236 r_chiral_restr 0.069 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10663 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing