4GEV

E. coli thymidylate synthase Y209W variant in complex with substrate and a cofactor analog


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4295vapor diffusion against 1.44 M Sodium citrate, HEPES from 5.2 mg/ml protein solution containing 17mM kPO4, DTT, 3.3 mM dUMP, 3.3 mM CB3717 and either 0.5% ethylacetate or 4% N-propanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.550.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.778α = 90
b = 125.778β = 90
c = 66.938γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103CCDADSC QUANTUM 210monochromator, double crystal Si (111)2002-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.0ALS8.3.1

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
11.345.83499.90.0825.19147002146991-3
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)
11.31.3299.90.8231.94.8

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.345.8341.34146990146990736299.820.12790.12670.1512
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]
-0.2432-0.24320.4864
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.316
f_angle_d1.348
f_chiral_restr0.082
f_bond_d0.008
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4310
Nucleic Acid Atoms
Solvent Atoms673
Heterogen Atoms110

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ELVESrefinement