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) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LCE | PDB ENTRY 1LCE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.4 | 293 | 4mg/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 | |
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Matthews coefficient | Solvent content |
2.73 | 54.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.518 | α = 90 |
b = 78.518 | β = 90 |
c = 224.377 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | 2005-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.008 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
1 | 2.4 | 50.32 | 99 | 0.095 | 0.095 | 5.6 | 10.32 | 16609 | 16609 | 1.4 | 55.434 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.4 | 2.53 | 99.1 | 0.528 | 0.528 | 1.4 | 10.69 | 2363 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1LCE | 2.4 | 50.32 | 1.4 | 15087 | 1505 | 100 | 0.25541 | 0.24827 | 0.32615 | RANDOM | 48.242 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.18 | 0.09 | 0.18 | -0.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.622 |
r_dihedral_angle_4_deg | 23.738 |
r_dihedral_angle_3_deg | 23.055 |
r_dihedral_angle_1_deg | 7.819 |
r_scangle_it | 3.225 |
r_angle_refined_deg | 2.201 |
r_scbond_it | 2.175 |
r_mcangle_it | 1.676 |
r_mcbond_it | 0.959 |
r_nbtor_refined | 0.32 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2383 |
Nucleic Acid Atoms | |
Solvent Atoms | 78 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |