4EZ8

Crystal structure of mouse thymidylate sythase in ternary complex with N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate and the cofactor product, dihydrofolate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP280MES, PEG 8K, MgAcetate, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.5151.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.121α = 90
b = 112.045β = 90
c = 88.297γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2011-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918BESSY14.1

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
11.1750990.0849.85.4118524117370-3
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)
11.171.1991.70.48835388

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.1721.35118524117324587299.040.10840.10720.1295RANDOM15.1112
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.057
r_dihedral_angle_4_deg18.325
r_dihedral_angle_3_deg12.12
r_scangle_it6.785
r_dihedral_angle_1_deg6.294
r_scbond_it4.888
r_mcangle_it3.388
r_mcbond_it2.341
r_rigid_bond_restr2.114
r_angle_refined_deg2.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.057
r_dihedral_angle_4_deg18.325
r_dihedral_angle_3_deg12.12
r_scangle_it6.785
r_dihedral_angle_1_deg6.294
r_scbond_it4.888
r_mcangle_it3.388
r_mcbond_it2.341
r_rigid_bond_restr2.114
r_angle_refined_deg2.013
r_angle_other_deg1.032
r_mcbond_other0.794
r_chiral_restr0.132
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2319
Nucleic Acid Atoms
Solvent Atoms478
Heterogen Atoms65

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction