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Staphylococcus aureus Type II pantothenate kinase in complex with a pantothenate analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EWS PDB entry 2EWS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 291 0.01 M inhibitor, 0.01 M magnesium chloride, 0.01 M ATP were added to the protein sample. 30% PEG4000, 0.2M magnesium chloride, 0.1M Tris hydrochloride, pH 8.5, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.92 α = 90 b = 136.53 β = 90 c = 73.62 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 ADSC QUANTUM 315 2011-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.42 68.265 98.1 0.086 14.1 9.7 53304 53304
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.5 96.5 0.736 0.736 1.1 7.5 7569
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB entry 2EWS 1.42 35 53298 2711 97.882 0.172 0.1713 0.1798 0.1942 0.2011 RANDOM 23.781
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] -0.095 -1.069 1.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.956 r_dihedral_angle_4_deg 15.234 r_dihedral_angle_3_deg 10.516 r_dihedral_angle_1_deg 5.617 r_angle_refined_deg 1.513 r_angle_other_deg 1.01 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_bond_other_d 0.006 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.956 r_dihedral_angle_4_deg 15.234 r_dihedral_angle_3_deg 10.516 r_dihedral_angle_1_deg 5.617 r_angle_refined_deg 1.513 r_angle_other_deg 1.01 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2054 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 66
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction