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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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.5 UL PROTEIN + 0.5 UL BUFFER (35% PEG3350, 0.1 M TRIS, 0.2 M MAGNESIUM CHLORIDE, PH 8.5)
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.387 α = 90 b = 136.746 β = 90 c = 73.947 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 RAYONIX MX-300 2016-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 1.4 43 100 0.087 13 9.3 57601
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 1.4 1.48 100 0.529 1.4 9.7
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 4M7X 1.4 43 54561 2950 99.86 0.1435 0.142 0.1515 0.174 0.1826 RANDOM 20.49
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] -0.15 0.35 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.617 r_sphericity_free 21.04 r_dihedral_angle_4_deg 18.644 r_sphericity_bonded 12.786 r_dihedral_angle_3_deg 10.705 r_dihedral_angle_1_deg 5.491 r_rigid_bond_restr 2.148 r_mcangle_it 1.658 r_angle_refined_deg 1.3 r_mcbond_it 1.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.617 r_sphericity_free 21.04 r_dihedral_angle_4_deg 18.644 r_sphericity_bonded 12.786 r_dihedral_angle_3_deg 10.705 r_dihedral_angle_1_deg 5.491 r_rigid_bond_restr 2.148 r_mcangle_it 1.658 r_angle_refined_deg 1.3 r_mcbond_it 1.155 r_mcbond_other 1.15 r_angle_other_deg 0.75 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2077 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 54
Software Software Software Name Purpose XDS data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction