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Crystal structure of an Oxidoreductase (short chain dehydrogenase/reductase family) from Brucella ovis in complex with a partially ordered NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X54 native structure, PDB entry 4X54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Mycrolytic MCSG1 screen, A10: 28% polypropylene glycol, 200mM CaCl2, 100mM HEPES/NaOH pH 7.5; BrovA.01365.b.B1.PS02128 at 19mg/ml, 3mM NADP; cryo: 15% PEG 400; tray 259821a10; puck hmh25-1
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.35 α = 90 b = 99.93 β = 90 c = 100.48 γ = 90
Symmetry Space Group I 2 2 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+ 2015-03-25 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 1.85 50 99.6 0.043 0.045 33.26 10.1 23344 23244 -3 23.05
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 1.85 1.9 99.9 0.52 0.57 3.15 6.01
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 native structure, PDB entry 4X54 1.85 47.12 1.34 23244 1916 99.58 0.1656 0.163 0.1637 0.1942 0.1948 Random selection 31.4154
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 12.545 f_angle_d 0.803 f_chiral_restr 0.055 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1622 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 40
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX phasing PHENIX refinement Coot model building PDB_EXTRACT data extraction