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Crystal structure of oxidoreductase (short chain dehydrogenase/reductase family) from Burkholderia thailandensis complexed with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 290 ButhA.00010.g.B1.PS01774 @ 20.96 mg/mL with 4mM NAD incubated at 16C; 28599c10 = JCSG+ C10: 0.1 M BICINE, pH 9.0, 10 % w/v PEG 20,000, 2 % v/v 1,4-Dioxane: Cryo = 25% EG: puck zvu9-7
Crystal Properties Matthews coefficient Solvent content 2.73 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.03 α = 90 b = 123.03 β = 90 c = 86.68 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 CCD RIGAKU SATURN 944+ 2017-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.15 46.453 99.9 0.084 0.09 0.999 15.86 8.244 36735 -3 32.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 99.8 0.527 0.572 0.885 3.71 6.662
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 4LVU 2.15 46.453 1.35 36677 1999 99.89 0.1624 0.1602 0.1616 0.1999 0.1994 38.7515
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 17.843 f_angle_d 0.848 f_chiral_restr 0.051 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3799 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 156
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction