5CGE

Structure of Hydroxyethylthiazole Kinase ThiM from Staphylococcus aureus in complex with substrate analog 2-(2-methyl-1H-imidazole-1-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 20 mM substrate analog 2-(2-methyl-1H-imidazole-1-yl)ethanol
Crystal Properties
Matthews coefficientSolvent content
2.3247.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.345α = 92.64
b = 62.483β = 92.05
c = 109.167γ = 101.46
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.976300PETRA 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
11.623093.410.73.6191461

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 DIFFRACTIONTHROUGHOUT1.6230181567950893.190.18340.182380.2028RANDOM29.176
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]
0.810.11-1.1-1.12-0.870.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.187
r_dihedral_angle_4_deg15.285
r_dihedral_angle_3_deg12.819
r_dihedral_angle_1_deg5.893
r_long_range_B_refined5.878
r_long_range_B_other5.867
r_scangle_other3.549
r_mcangle_it2.454
r_mcangle_other2.454
r_scbond_it2.372
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.187
r_dihedral_angle_4_deg15.285
r_dihedral_angle_3_deg12.819
r_dihedral_angle_1_deg5.893
r_long_range_B_refined5.878
r_long_range_B_other5.867
r_scangle_other3.549
r_mcangle_it2.454
r_mcangle_other2.454
r_scbond_it2.372
r_scbond_other2.372
r_angle_refined_deg1.699
r_mcbond_it1.585
r_mcbond_other1.581
r_angle_other_deg1.452
r_chiral_restr0.111
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_bond_other_d0.009
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 Atoms11453
Nucleic Acid Atoms
Solvent Atoms506
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing