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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 4M7X PDB entry 4m7x
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 0.01 M inhibitor, 0.01 M magnesium chloride, 0.01 M ATP were added to the protein sample. Crystal condition: 2.5 M ammonium sulfate, 0.1 M BTP, 1.1 % w/v Cyclohexylethanoyl-N-hydroxyethylglucamide., pH 7.0, vapor diffusion
Crystal Properties Matthews coefficient Solvent content 2.3 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.96 α = 90 b = 56.13 β = 101.17 c = 68.42 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 IMAGE PLATE RIGAKU RAXIS 2011-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 1.8 30 99.4 0.079 14.87 48878 -3 33.94
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 1.8 1.85 99 0.95 2
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 4m7x 1.8 26.532 48796 2074 99.227 0.178 0.1761 0.1864 0.2198 0.229 thin shells (sftools) 31.734
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] 2.136 -0.599 -0.646 -1.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.499 r_dihedral_angle_4_deg 15.775 r_dihedral_angle_3_deg 11.434 r_dihedral_angle_1_deg 5.436 r_angle_refined_deg 1.541 r_angle_other_deg 0.751 r_chiral_restr 0.076 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.499 r_dihedral_angle_4_deg 15.775 r_dihedral_angle_3_deg 11.434 r_dihedral_angle_1_deg 5.436 r_angle_refined_deg 1.541 r_angle_other_deg 0.751 r_chiral_restr 0.076 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3950 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 159
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction