5FCT

Mouse thymidylate synthase in ternary complex with FdUMP and methylenetetrahydrofolate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EZ8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP280MES, PEG 8K, MgAcetate
Crystal Properties
Matthews coefficientSolvent content
2.1442.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.224α = 90
b = 83.302β = 105.43
c = 68.85γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAGILENT ATLAS CCD2013-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEAgilent SuperNova1.5406

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
11.5526.1499.970.068145.985416
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)
11.551.631000.5172.44

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 REPLACEMENTTHROUGHOUT4EZ81.5526.1481162427799.970.119720.117260.16614RANDOM17.752
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]
-0.030.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.039
r_sphericity_free27.562
r_dihedral_angle_4_deg18.898
r_dihedral_angle_3_deg12.359
r_sphericity_bonded9.844
r_dihedral_angle_1_deg6.077
r_long_range_B_refined3.885
r_long_range_B_other3.222
r_scangle_other2.883
r_scbond_it2.459
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.039
r_sphericity_free27.562
r_dihedral_angle_4_deg18.898
r_dihedral_angle_3_deg12.359
r_sphericity_bonded9.844
r_dihedral_angle_1_deg6.077
r_long_range_B_refined3.885
r_long_range_B_other3.222
r_scangle_other2.883
r_scbond_it2.459
r_scbond_other2.458
r_mcangle_it1.914
r_mcangle_other1.914
r_rigid_bond_restr1.841
r_mcbond_other1.493
r_mcbond_it1.492
r_angle_refined_deg1.415
r_angle_other_deg0.775
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4638
Nucleic Acid Atoms
Solvent Atoms661
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
CrysalisProphasing