1TDU
E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE (DURD)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZPR | PDB ENTRY 1ZPR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.8 | CRYSTALLIZATION WAS CONDUCTED IN HANGING DROPS CONTAINING 4.2 MG/ML E. COLI TS, 0.38 MM DURD, 3.8 MM DTT, 1.0 MM CB3717 AND 1.2 M (NH4)2SO4, PH 7.8 (20 MM KPO4) OVER A WELL SOLUTION CONTAINING 2.4 M (NH4)2SO4 AND 1.0 MM DTT., vapor diffusion - hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 52.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.299 | α = 90 |
b = 127.299 | β = 90 |
c = 67.983 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | 298 | IMAGE PLATE | RIGAKU | 1996-11-06 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH2R |
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 | 2.1 | 50 | 95.2 | 0.064 | 0.064 | 15.9 | 4.8 | 36809 | 17.6 |
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) | ||||||||||
2.1 | 2.16 | 90.2 | 0.278 | 0.278 | 3.6 | 3.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | DIFFERENCE FOURIER | THROUGHOUT | PDB ENTRY 1ZPR | 2.1 | 8 | 2 | 28316 | 2833 | 78.4 | 0.185 | 0.185 | 0.246 | SHELLS | 25.5 |
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 | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 25.5 |
x_scangle_it | 3.32 |
x_angle_deg | 2.9 |
x_scbond_it | 2.18 |
x_mcangle_it | 2.01 |
x_mcbond_it | 1.21 |
x_improper_angle_d | 1.18 |
x_bond_d | 0.012 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4298 |
Nucleic Acid Atoms | |
Solvent Atoms | 153 |
Heterogen Atoms | 105 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |