2VF0
CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH 5NO2DUMP AND BW1843U89
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7.5 | 20 MM POTASSIUM PHOSPHATE BUFFER, 4 MM DTT AND INCREMENTS IN AMMONIUM SULFATE FROM 2.05 TO 2.6 M, PH 7.5 TO 8 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.6 | 54 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 127.16 | α = 90 |
b = 127.16 | β = 90 |
c = 67.95 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 298 | AREA DETECTOR | ENRAF-NONIUS | 1999-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | ENRAF-NONIUS FR571 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.7 | 35.58 | 95.1 | 0.17 | 3.7 | 4.7 | 15793 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRIES 1FFL AND 1FWM | 3 | 33.98 | 12094 | 611 | 95.1 | 0.18 | 0.18 | 0.239 | RANDOM | 20.1 |
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] | |
-3.18 | -3.18 | 6.37 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.3 |
c_scangle_it | 2.36 |
c_mcangle_it | 1.73 |
c_scbond_it | 1.45 |
c_angle_deg | 1.4 |
c_mcbond_it | 0.99 |
c_improper_angle_d | 0.9 |
c_bond_d | 0.009 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4306 |
Nucleic Acid Atoms | |
Solvent Atoms | 29 |
Heterogen Atoms | 125 |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
MADNESS | data reduction |
PROCOR | data reduction |
Agrovata | data scaling |
ROTAVATA | data scaling |
SCALA | data scaling |
TRUNCATE | data scaling |
X-PLOR | phasing |