5CGA

Structure of Hydroxyethylthiazole kinase ThiM from Staphylococcus aureus in complex with substrate analog 2-(1,3,5-trimethyl-1H-pyrazole-4-yl)ethanol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293.218 - 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 coefficientSolvent content
2.2946.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.026α = 92.59
b = 62.362β = 91.39
c = 108.32γ = 101.28
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.976262PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.873095.812.73.6125936

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8729.81119598633795.790.17010.168620.19899RANDOM35.128
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]
-0.53-0.49-0.37-0.89-0.271.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.002
r_dihedral_angle_4_deg15.503
r_dihedral_angle_3_deg12.63
r_long_range_B_refined5.847
r_long_range_B_other5.788
r_dihedral_angle_1_deg5.757
r_scangle_other3.411
r_mcangle_it2.474
r_mcangle_other2.474
r_scbond_it2.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.002
r_dihedral_angle_4_deg15.503
r_dihedral_angle_3_deg12.63
r_long_range_B_refined5.847
r_long_range_B_other5.788
r_dihedral_angle_1_deg5.757
r_scangle_other3.411
r_mcangle_it2.474
r_mcangle_other2.474
r_scbond_it2.325
r_scbond_other2.325
r_angle_refined_deg1.738
r_mcbond_it1.682
r_mcbond_other1.68
r_angle_other_deg1.453
r_chiral_restr0.116
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.01
r_gen_planes_other0.009
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 AtomsNumber
Protein Atoms11228
Nucleic Acid Atoms
Solvent Atoms486
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing