3C0A

Lactobacillus CASEI Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative 14C in Multiple Binding Modes-Mode 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LCEPDB ENTRY 1LCE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42934mg/mL LcTS, 1mM EDTA, 40mM dUMP, 20mM TRIS HCl,100mM ammonium phosphate, 5% PEG 400 v/v, 10-12% ligand solution in DMSO, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7354.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.518α = 90
b = 78.518β = 90
c = 224.377γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.008ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.450.32990.0950.0955.610.3216609166091.455.434
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5399.10.5280.5281.410.692363

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1LCE2.450.321.41508715051000.255410.248270.32615RANDOM48.242
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]
0.180.090.18-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.622
r_dihedral_angle_4_deg23.738
r_dihedral_angle_3_deg23.055
r_dihedral_angle_1_deg7.819
r_scangle_it3.225
r_angle_refined_deg2.201
r_scbond_it2.175
r_mcangle_it1.676
r_mcbond_it0.959
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.622
r_dihedral_angle_4_deg23.738
r_dihedral_angle_3_deg23.055
r_dihedral_angle_1_deg7.819
r_scangle_it3.225
r_angle_refined_deg2.201
r_scbond_it2.175
r_mcangle_it1.676
r_mcbond_it0.959
r_nbtor_refined0.32
r_nbd_refined0.253
r_symmetry_vdw_refined0.241
r_xyhbond_nbd_refined0.204
r_chiral_restr0.136
r_symmetry_hbond_refined0.091
r_bond_refined_d0.019
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2383
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing