4ECM

2.3 Angstrom Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase from Bacillus anthracis in Complex with Thymidine-5-diphospho-alpha-D-glucose and Pyrophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HL3PDB entry 3HL3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5295Protein: 7.5 mg/mL, 0.5M NaCl, 0.01M Tris-HCl (pH 8.3), 0.001M Thymidine-5-diphospho-alpha-D-glucose. Screen: PACT (H8), 0.2 Sodium Sulfate, 0.1M TRIS propane, 20% (w/v) PEG 33500, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.766.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.072α = 90
b = 135.072β = 90
c = 85.138γ = 120
Symmetry
Space GroupP 6 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium lenses2012-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
12.33099.90.10822.910.72093820938-332.4
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)
12.32.341000.5335.110.91022

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3HL32.329.241977519775107399.920.154420.154420.152710.18588RANDOM24.768
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]
-0.26-0.13-0.260.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.567
r_dihedral_angle_4_deg19.929
r_dihedral_angle_3_deg10.423
r_scangle_it4.551
r_dihedral_angle_1_deg3.556
r_scbond_it3.009
r_mcangle_it1.93
r_angle_refined_deg1.526
r_mcbond_it1.044
r_angle_other_deg0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.567
r_dihedral_angle_4_deg19.929
r_dihedral_angle_3_deg10.423
r_scangle_it4.551
r_dihedral_angle_1_deg3.556
r_scbond_it3.009
r_mcangle_it1.93
r_angle_refined_deg1.526
r_mcbond_it1.044
r_angle_other_deg0.85
r_mcbond_other0.285
r_chiral_restr0.111
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1940
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms45

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling