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Structure of Hydroxyethylthiazole Kinase ThiM from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C3Q
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),
Crystal Properties Matthews coefficient Solvent content 2.25 45.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.561 α = 90 b = 103.519 β = 99.48 c = 126.18 γ = 90
Symmetry Space Group P 1 21 1
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 2011-12-19 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 2.09 20 99.9 0.078 13.4 7.8 93740
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1C3Q 2.09 20 88976 4693 99.82 0.20479 0.20342 0.2304 0.2226 RANDOM 38.648
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] -2.76 -1.24 6.68 -3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.569 r_dihedral_angle_3_deg 15.54 r_dihedral_angle_4_deg 11.76 r_dihedral_angle_1_deg 6.521 r_long_range_B_refined 5.909 r_long_range_B_other 5.862 r_scangle_other 2.835 r_mcangle_it 2.382 r_mcangle_other 2.382 r_scbond_it 1.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.569 r_dihedral_angle_3_deg 15.54 r_dihedral_angle_4_deg 11.76 r_dihedral_angle_1_deg 6.521 r_long_range_B_refined 5.909 r_long_range_B_other 5.862 r_scangle_other 2.835 r_mcangle_it 2.382 r_mcangle_other 2.382 r_scbond_it 1.773 r_scbond_other 1.773 r_angle_refined_deg 1.615 r_angle_other_deg 1.455 r_mcbond_it 1.452 r_mcbond_other 1.45 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.007 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 11439 Nucleic Acid Atoms Solvent Atoms 552 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing