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Structure of Hydroxyethylthiazole Kinase ThiM from Staphylococcus aureus in complex with substrate analog 2-(2-methyl-1H-imidazole-1-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 20 mM substrate analog 2-(2-methyl-1H-imidazole-1-yl)ethanol
Crystal Properties Matthews coefficient Solvent content 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.345 α = 92.64 b = 62.483 β = 92.05 c = 109.167 γ = 101.46
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-F 2013-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976300 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 1.62 30 93.4 10.7 3.6 191461
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 1.62 30 181567 9508 93.19 0.1834 0.18238 0.1908 0.2028 0.2083 RANDOM 29.176
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] 0.81 0.11 -1.1 -1.12 -0.87 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.187 r_dihedral_angle_4_deg 15.285 r_dihedral_angle_3_deg 12.819 r_dihedral_angle_1_deg 5.893 r_long_range_B_refined 5.878 r_long_range_B_other 5.867 r_scangle_other 3.549 r_mcangle_it 2.454 r_mcangle_other 2.454 r_scbond_it 2.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.187 r_dihedral_angle_4_deg 15.285 r_dihedral_angle_3_deg 12.819 r_dihedral_angle_1_deg 5.893 r_long_range_B_refined 5.878 r_long_range_B_other 5.867 r_scangle_other 3.549 r_mcangle_it 2.454 r_mcangle_other 2.454 r_scbond_it 2.372 r_scbond_other 2.372 r_angle_refined_deg 1.699 r_mcbond_it 1.585 r_mcbond_other 1.581 r_angle_other_deg 1.452 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.009 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 11453 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing