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Crystal Structure of Galactonate dehydratase from Brucella melitensis biovar Abortus 2308
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OYN MR-rosetta starting from PDB entry 5OYN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 RigakuReagents JCSG+ screen, condition b10 200mM Magnesium chloride, 100mM sodium cacodylate pH 6.5, 20% (w/V) PEG 3350: BrabA.18180.a.B1.PS02071 at 27.12mg/ml: tray 256086 b10: cryo: direct: puck bvd7-1.
Crystal Properties Matthews coefficient Solvent content 3.84 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.95 α = 90 b = 144.95 β = 90 c = 167.57 γ = 120
Symmetry Space Group P 62 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 RAYONIX MX-300 Beryllium Lenses 2014-04-27 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) 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 2.3 50 99.9 0.087 0.09 0.999 19.95 14.887 46675 47.905
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 2.3 2.36 100 0.585 0.604 0.954 4.2 15.476
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 MR-rosetta starting from PDB entry 5OYN 2.3 44.24 1.34 46610 2037 99.94 0.1816 0.1804 0.1805 0.2083 0.2075 0 59.53
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 12.9752 f_angle_d 0.7568 f_chiral_restr 0.0485 f_plane_restr 0.0068 f_bond_d 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4243 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 38
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MR-Rosetta phasing PHENIX model building Coot model building