4HO4

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1M Tris, 1.9M lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8356.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.24α = 90
b = 90.81β = 125.05
c = 87.754γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315rmirrors2012-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0000NSRRCBL13B1

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
11.643099.40.0421.1588977
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)
11.641.799.80.3295

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entry 1H5R1.643088917446099.20.1940.1930.22326.99
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]
-0.93-1.10.71-1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.851
r_dihedral_angle_4_deg22.708
r_dihedral_angle_3_deg14.701
r_dihedral_angle_1_deg6.93
r_scangle_it6.236
r_scbond_it3.975
r_mcangle_it2.787
r_mcbond_it1.75
r_angle_refined_deg1.566
r_chiral_restr0.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.851
r_dihedral_angle_4_deg22.708
r_dihedral_angle_3_deg14.701
r_dihedral_angle_1_deg6.93
r_scangle_it6.236
r_scbond_it3.975
r_mcangle_it2.787
r_mcbond_it1.75
r_angle_refined_deg1.566
r_chiral_restr0.136
r_bond_refined_d0.018
r_gen_planes_refined0.017
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4583
Nucleic Acid Atoms
Solvent Atoms496
Heterogen Atoms104

Software

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