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Crystal structure of a putative Putative D-beta-hydroxybutyrate dehydrogenase from Burkholderia cenocepacia J2315
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V2H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Microlytics MCSG1 screen F1: 20% PEG MME 5000, 100mM BisTris pH 6.5, cryo protected with 20% EG in two steps, then annealed in cryostream; BuceA.00010.z.B1.PS01812 at 26.7 mg/ml; tray 246271, puck tye 7-7
Crystal Properties Matthews coefficient Solvent content 2.43 49.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.22 α = 90 b = 91.95 β = 92.94 c = 116.56 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN 944+ 2013-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 50 98.6 0.08 0.084 19.45 8.79 168840 -3 19.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 90.2 0.545 0.635 2.62 3.67
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3v2h 1.9 48.049 1.99 168817 8451 98.57 0.185 0.183 0.1851 0.2223 0.2239 Random selection 33.2067
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 12.375 f_angle_d 0.957 f_chiral_restr 0.04 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14304 Nucleic Acid Atoms Solvent Atoms 1240 Heterogen Atoms 46
Software Software Software Name Purpose CrystalClear data collection XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing PHENIX refinement