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Structure of Hydroxyethylthiazole kinase ThiM from Staphylococcus aureus in complex with native substrate 2-(4-methyl-1,3-thiazol-5-yl)ethanol.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.2 18 - 22 % PEG 3,350 (w/v), 0.2 M magnesium formate, 5 % isopropanol (v/v), soaked with 0.5 mM 2-(4-methyl-1,3-thiazol-5-yl)ethanol
Crystal Properties Matthews coefficient Solvent content 2.33 47.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.549 α = 92.18 b = 62.741 β = 91.44 c = 108.459 γ = 101.32
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 MAR CCD 165 mm 2012-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81 EMBL/DESY, HAMBURG X13
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 1.9 20 94.7 0.027 21.8 2 119565
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 THROUGHOUT 1.9 20 117078 6189 97.59 0.18729 0.18615 0.1947 0.20951 0.2162 RANDOM 37.845
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] 0.77 -0.23 -1.79 -1.97 -2.1 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.035 r_dihedral_angle_4_deg 20.371 r_dihedral_angle_3_deg 13.555 r_dihedral_angle_1_deg 6.565 r_long_range_B_refined 5.212 r_long_range_B_other 5.184 r_scangle_other 2.655 r_mcangle_it 2.061 r_mcangle_other 2.05 r_scbond_it 1.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.035 r_dihedral_angle_4_deg 20.371 r_dihedral_angle_3_deg 13.555 r_dihedral_angle_1_deg 6.565 r_long_range_B_refined 5.212 r_long_range_B_other 5.184 r_scangle_other 2.655 r_mcangle_it 2.061 r_mcangle_other 2.05 r_scbond_it 1.741 r_scbond_other 1.741 r_angle_refined_deg 1.598 r_angle_other_deg 1.395 r_mcbond_it 1.282 r_mcbond_other 1.282 r_chiral_restr 0.101 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.008 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 11149 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing