3BYX

Lactobacillus CASEI Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00 in Multiple Binding Modes


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42931mM EDTA, 100mM ammonium phosphate, 5% (v/v) PEG 400, 20mM Tris-HCl, DMSO, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.550.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.012α = 90
b = 77.012β = 90
c = 213.97γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-02-15MSINGLE 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
12.448.7484.40.0950.09575.413142130701.938.664
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)
12.42.5385.60.4150.4151.96.471470

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1LCA2.448.7412429124296411000.2080.2080.2040.283RANDOM34.059
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.049
r_dihedral_angle_3_deg22.656
r_dihedral_angle_4_deg18.565
r_dihedral_angle_1_deg7.369
r_scangle_it2.226
r_angle_refined_deg1.928
r_scbond_it1.507
r_mcangle_it1.186
r_mcbond_it0.659
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.049
r_dihedral_angle_3_deg22.656
r_dihedral_angle_4_deg18.565
r_dihedral_angle_1_deg7.369
r_scangle_it2.226
r_angle_refined_deg1.928
r_scbond_it1.507
r_mcangle_it1.186
r_mcbond_it0.659
r_nbtor_refined0.315
r_nbd_refined0.234
r_xyhbond_nbd_refined0.181
r_symmetry_vdw_refined0.179
r_chiral_restr0.12
r_symmetry_hbond_refined0.101
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2568
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms45

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction