5X67

Human thymidylate synthase in complex with dUMP and nolatrexed


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I00 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298100mM sodium calcodylate, pH 6.5, 25% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.3547.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.29α = 90
b = 108.29β = 90
c = 106.034γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX21.0130Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.1348.2299.50.1770.1830.0460.99815.515.835533
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.132.294.40.8670.8970.2280.873152718

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 REPLACEMENTTHROUGHOUT1I002.1348.2233804169399.530.1560.15350.2065RANDOM22.127
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]
-0.52-0.521.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.695
r_dihedral_angle_4_deg20.55
r_dihedral_angle_3_deg13.352
r_dihedral_angle_1_deg6.285
r_angle_refined_deg1.874
r_angle_other_deg1.041
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.695
r_dihedral_angle_4_deg20.55
r_dihedral_angle_3_deg13.352
r_dihedral_angle_1_deg6.285
r_angle_refined_deg1.874
r_angle_other_deg1.041
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4593
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata processing
PHASERphasing
XDSdata reduction