1AXW

E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH METHOTREXATE (MTX) AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KCEPDB ENTRY 1KCE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.84.2 MG/ML E.COLI TS, 0.38 MM DUMP, 3.8 MM DTT, 1.0 MM MTX AND 1.2 M (NH4)2SO4, PH 7.8 (20 MM KPO4) OVER 2.4 M (NH4)2SO4 AND 1.0 MM DTT
Crystal Properties
Matthews coefficientSolvent content
2.5652.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.34α = 90
b = 127.34β = 90
c = 68.06γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray278IMAGE PLATERIGAKU RAXIS IIC1996-11-25M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R

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
11.75078.30.09167.969189110.5
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)
1.71.7570.10.34433

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONDIFFERENCE FOURIERTHROUGHOUTPDB ENTRY 1KCE1.750269189436378.30.2170.2170.265SHELLS29
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d25.2
x_scangle_it5.86
x_mcangle_it4.22
x_scbond_it3.96
x_mcbond_it2.98
x_angle_deg1.5
x_improper_angle_d1.18
x_bond_d0.008
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d25.2
x_scangle_it5.86
x_mcangle_it4.22
x_scbond_it3.96
x_mcbond_it2.98
x_angle_deg1.5
x_improper_angle_d1.18
x_bond_d0.008
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4306
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms118

Software

Software
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing