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Structure of Hydroxyethylthiazole kinase ThiM from Staphylococcus aureus in complex with substrate analog 2-(1,3,5-trimethyl-1H-pyrazole-4-yl)ethanol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.2 18 - 22 % PEG 3,350 (w/v), 0.2 M magnesium formate, 5 % isopropanol (v/v), soaked with 25 mM substrate analog 2-(1,3,5-trimethyl-1H-pyrazole-4-yl)ethanol
Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.026 α = 92.59 b = 62.362 β = 91.39 c = 108.32 γ = 101.28
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976262 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.87 30 95.8 12.7 3.6 125936
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 MOLECULAR REPLACEMENT THROUGHOUT 1.87 29.81 119598 6337 95.79 0.1701 0.16862 0.1755 0.19899 0.2047 RANDOM 35.128
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] -0.53 -0.49 -0.37 -0.89 -0.27 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.002 r_dihedral_angle_4_deg 15.503 r_dihedral_angle_3_deg 12.63 r_long_range_B_refined 5.847 r_long_range_B_other 5.788 r_dihedral_angle_1_deg 5.757 r_scangle_other 3.411 r_mcangle_it 2.474 r_mcangle_other 2.474 r_scbond_it 2.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.002 r_dihedral_angle_4_deg 15.503 r_dihedral_angle_3_deg 12.63 r_long_range_B_refined 5.847 r_long_range_B_other 5.788 r_dihedral_angle_1_deg 5.757 r_scangle_other 3.411 r_mcangle_it 2.474 r_mcangle_other 2.474 r_scbond_it 2.325 r_scbond_other 2.325 r_angle_refined_deg 1.738 r_mcbond_it 1.682 r_mcbond_other 1.68 r_angle_other_deg 1.453 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.01 r_gen_planes_other 0.009 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11228 Nucleic Acid Atoms Solvent Atoms 486 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing