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Crystal Structure of Urease subunit gamma 2 from Brucella melitensis biovar Abortus 2308
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2KAU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 Morpheus B2: 0.1 M Imidazole/MES pH 6.50, 0.09 M sodium fluoride, 0.09 M sodium bromide, 0.09 M sodium iodide, 30% ethylene glycol, 30% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.07 59.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.51 α = 90 b = 145.01 β = 90 c = 137.18 γ = 90
Symmetry Space Group C 2 2 21
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+ 2012-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 50 98.6 0.087 14.8 48876 48192 -3 31.178
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 2.1 2.15 90.5 0.354 4.37
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT 2KAU 2.1 50 48876 48192 2374 97.88 0.1527 0.1527 0.1509 0.1713 0.1878 0.1989 RANDOM 30.876
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] -16 -19.81 35.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.642 r_dihedral_angle_4_deg 14.959 r_dihedral_angle_3_deg 13.854 r_dihedral_angle_1_deg 4.683 r_angle_refined_deg 1.444 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4493 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 17
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction