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Crystal Structure of Ribose-5-phosphate Isomerase from Brucella melitensis 16M
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 290 MCSG-1 a5(250341a5): 0.2 M Sodium Chloride, 0.1 M Sodium Acetate: Acetic Acid pH 4.5, 1.26 M Ammomium Sulfate;
cryo: 20% GLYCEROL; BrmeA.00966.a.B1.PW37380 at 25.8 mg/ml, puck twt3-5
Crystal Properties Matthews coefficient Solvent content 2.09 41.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.57 α = 90 b = 51.57 β = 90 c = 177.29 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 MARMOSAIC 225 mm CCD Beryllium Lenses 2014-04-03 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 1.6 44.935 98.7 0.04 0.999 26.12 7.81 32358 -3 22.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 99.8 0.482 3.5 7.97
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 3he8 1.6 44.323 1.35 162986 32247 2112 98.67 0.1827 0.1807 0.1812 0.2115 0.2105 33.0413
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 8.703 f_angle_d 0.697 f_chiral_restr 0.048 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1659 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing