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Crystal structure of S.aureus pantothenate kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 PEG 2K MME 28%, 0.1M Bis-Tris 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.044 α = 90 b = 104.044 β = 90 c = 85.718 γ = 120
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 SBC-3 2005-08-09 M SINGLE WAVELENGTH 2 1 x-ray CCD SBC-3 2005-08-03 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9 APS 19-BM 2 SYNCHROTRON APS BEAMLINE 19-BM 0.97972, 0.97983 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1,2 2.05 50 99.8 0.031 0.044 59.8 10.4 33134 33134 1 1
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) 1,2 2.05 2.12 100 0.374 0.392 7.1 10.6 3292
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.05 50 31335 1667 99.36 0.21926 0.21554 0.2247 0.28914 0.2103 RANDOM 38.541
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] -0.11 -0.06 -0.11 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.518 r_dihedral_angle_4_deg 22.715 r_dihedral_angle_3_deg 19.545 r_dihedral_angle_1_deg 7.133 r_scangle_it 5.132 r_scbond_it 3.54 r_angle_refined_deg 2.458 r_mcangle_it 2.439 r_mcbond_it 1.569 r_symmetry_hbond_refined 0.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.518 r_dihedral_angle_4_deg 22.715 r_dihedral_angle_3_deg 19.545 r_dihedral_angle_1_deg 7.133 r_scangle_it 5.132 r_scbond_it 3.54 r_angle_refined_deg 2.458 r_mcangle_it 2.439 r_mcbond_it 1.569 r_symmetry_hbond_refined 0.682 r_symmetry_vdw_refined 0.356 r_nbtor_refined 0.319 r_xyhbond_nbd_refined 0.305 r_nbd_refined 0.281 r_chiral_restr 0.222 r_metal_ion_refined 0.087 r_bond_refined_d 0.028 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3962 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing MOLREP phasing