4HO2

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with thymidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H5RPDB entry 1H5R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M sodium cacodylate, 2.0M lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.895α = 90
b = 91.895β = 90
c = 70.134γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315rmirrors2011-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C11.0000NSRRCBL13C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.843099.50.04212.72652526483
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.841.911000.35713

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB entry 1H5R1.843026483133499.480.19540.19340.2324RANDOM30.1519
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]
0.190.19-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.597
r_dihedral_angle_4_deg25.23
r_dihedral_angle_3_deg16.404
r_dihedral_angle_1_deg7.078
r_mcangle_it2.358
r_angle_refined_deg1.568
r_mcbond_it1.437
r_chiral_restr0.17
r_bond_refined_d0.019
r_gen_planes_refined0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.597
r_dihedral_angle_4_deg25.23
r_dihedral_angle_3_deg16.404
r_dihedral_angle_1_deg7.078
r_mcangle_it2.358
r_angle_refined_deg1.568
r_mcbond_it1.437
r_chiral_restr0.17
r_bond_refined_d0.019
r_gen_planes_refined0.013
r_scbond_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2256
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing