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Crystal structure of a short-chain dehydrogenase/reductase from Vibrio parahaemolyticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.4 294 100mM Bis-Tris pH 5.4, 15% PEG 3350, 100mM magnesium chloride, vapor diffusion, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.814 α = 72.38 b = 71.315 β = 89.39 c = 93.075 γ = 74.3
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 MAR CCD 165 mm 2009-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 88.44 96.9 0.089 0.089 7.3 2.4 127600 123644 23.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 95.5 0.324 0.324 2.1 2.4 17750
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.9 20 127464 123564 6218 96.94 0.202 0.2 0.2054 0.249 0.2505 RANDOM 32.568
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] -0.7 0.55 0.7 0.04 -0.35 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.004 r_dihedral_angle_3_deg 15.865 r_dihedral_angle_4_deg 13.156 r_dihedral_angle_1_deg 5.96 r_scangle_it 4.311 r_scbond_it 2.666 r_mcangle_it 1.677 r_angle_refined_deg 1.557 r_angle_other_deg 0.961 r_mcbond_it 0.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.004 r_dihedral_angle_3_deg 15.865 r_dihedral_angle_4_deg 13.156 r_dihedral_angle_1_deg 5.96 r_scangle_it 4.311 r_scbond_it 2.666 r_mcangle_it 1.677 r_angle_refined_deg 1.557 r_angle_other_deg 0.961 r_mcbond_it 0.934 r_mcbond_other 0.236 r_chiral_restr 0.094 r_bond_refined_d 0.017 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 12733 Nucleic Acid Atoms Solvent Atoms 586 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXCD phasing SHELXE model building