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Crystal Structure of an Oxidoreductase (short chain dehydrogenase/reductase family) from Burkholderia thailandensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 ButhA.00010.z.B1.PS02557 at 3.46 mg/ml, mixed 1:1 with an equal volume MCSG1(g5): 0.1 M Bis-Tris:HCl, pH=6.5, 2.0 M ammonium sulfate, cryoprotected with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.15 42.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.69 α = 90 b = 109.08 β = 99.65 c = 73.53 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 Beryllium Lenses 2016-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 50 99.6 0.057 0.999 16.11 3.8 50699 -3 16.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 100 0.506 0.854 2.66 14162
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 FREE R-VALUE 5JC8 1.7 45.428 1.35 50686 2023 99.59 0.1627 0.1615 0.177 0.1923 0.2005 22.1227
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 10.552 f_angle_d 0.734 f_chiral_restr 0.051 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3593 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 114
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing XDS data reduction