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2.05 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with alpha-ketoglutarate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 Protein: 7.1 mg/mL, 0.25M Sodium chloride, Tris-HCl pH 8.3, Screen: PEGs II (C11), 0.2M Lithium sulfate, 0.1M Tris pH 8.5, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.7 54.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.444 α = 90 b = 84.689 β = 116.91 c = 95.966 γ = 90
Symmetry Space Group C 1 2 1
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 300 mm CCD Beryllium lenses 2010-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.05 30 98.8 0.066 13.4 3.7 40617 40617 -3 41.8
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) 2.05 2.09 88.9 0.489 2.05 2.9 1827
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.05 29.2 36636 36636 1928 95.05 0.17557 0.17557 0.17323 0.1854 0.22146 0.2285 RANDOM 49.413
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] -2.51 -2.53 2.37 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.013 r_dihedral_angle_3_deg 9.207 r_dihedral_angle_4_deg 7.853 r_scangle_it 4.594 r_scbond_it 3.09 r_dihedral_angle_1_deg 2.95 r_mcangle_it 1.9 r_angle_refined_deg 1.426 r_mcbond_it 1.101 r_angle_other_deg 0.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.013 r_dihedral_angle_3_deg 9.207 r_dihedral_angle_4_deg 7.853 r_scangle_it 4.594 r_scbond_it 3.09 r_dihedral_angle_1_deg 2.95 r_mcangle_it 1.9 r_angle_refined_deg 1.426 r_mcbond_it 1.101 r_angle_other_deg 0.818 r_mcbond_other 0.313 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4092 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 23
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing