3C06

Lactobacillus CASEI Thymidylate Synthase Ternary Complex With DUMP and the Phtalimidic Derivative 14C in Multiple Binding Modes-Mode 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LCAPDB ENTRY 1LCA

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
2.4650

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.573α = 90
b = 76.573β = 90
c = 212.931γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.930ESRFID14-1

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
12.638.2998.60.10.16.48.411884118841.757.048
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)
12.62.7499.60.4340.4341.791700

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1LCA2.638.2911884113125651000.222120.218640.29179RANDOM40.999
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]
0.110.050.11-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.782
r_dihedral_angle_4_deg24.888
r_dihedral_angle_3_deg23.765
r_dihedral_angle_1_deg7.953
r_scangle_it2.903
r_angle_refined_deg2.115
r_scbond_it1.994
r_mcangle_it1.543
r_mcbond_it0.856
r_nbtor_refined0.327
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.782
r_dihedral_angle_4_deg24.888
r_dihedral_angle_3_deg23.765
r_dihedral_angle_1_deg7.953
r_scangle_it2.903
r_angle_refined_deg2.115
r_scbond_it1.994
r_mcangle_it1.543
r_mcbond_it0.856
r_nbtor_refined0.327
r_symmetry_hbond_refined0.262
r_nbd_refined0.258
r_symmetry_vdw_refined0.246
r_xyhbond_nbd_refined0.19
r_chiral_restr0.126
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2487
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing