3BZ0

Lactobacillus Casei Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00


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, 20 mM Tris-HCl, dUMP, 100mM ammonium phopshate, 5% (v/v) PEG 400, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6854.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.916α = 90
b = 77.916β = 90
c = 224.183γ = 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
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B1.078EMBL/DESY, HAMBURGBW7B

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
12.733.3788.60.1390.1394.3410447104431.756.53
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)
12.72.8592.30.4390.4391.74.11502

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 1LCA2.733.3710443951193288.60.23490.225820.32619RANDOM37.422
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]
0.020.010.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.425
r_dihedral_angle_3_deg24.324
r_dihedral_angle_4_deg23.758
r_dihedral_angle_1_deg8.06
r_scangle_it2.955
r_angle_refined_deg2.151
r_scbond_it1.933
r_mcangle_it1.518
r_mcbond_it0.86
r_nbtor_refined0.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.425
r_dihedral_angle_3_deg24.324
r_dihedral_angle_4_deg23.758
r_dihedral_angle_1_deg8.06
r_scangle_it2.955
r_angle_refined_deg2.151
r_scbond_it1.933
r_mcangle_it1.518
r_mcbond_it0.86
r_nbtor_refined0.331
r_symmetry_vdw_refined0.329
r_nbd_refined0.284
r_symmetry_hbond_refined0.216
r_xyhbond_nbd_refined0.166
r_chiral_restr0.154
r_bond_refined_d0.019
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2521
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing