5FUW
catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP or dThd
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5FUV | PDB ENTRY 5FUV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 0.1 M HEPES PH 7.0, 0.8 M SUCCINIC ACID 1 MM TMP, 1 MM APPNHP, 3 MM MGCL2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.77 | 67 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 114.999 | ¦Á = 90 |
b = 114.999 | ¦Â = 90 |
c = 104.77 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 43 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 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.2 | 64.24 | 100 | 0.1 | 11.8 | 11.6 | 36299 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.27 | 100 | 0.88 | 2.6 | 10.8 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 5FUV | 2.2 | 115 | 34470 | 1757 | 99.88 | 0.1861 | 0.18532 | 0.20126 | RANDOM | 55.707 |
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] | |
-1.23 | -1.23 | 2.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.005 |
r_dihedral_angle_3_deg | 12.572 |
r_long_range_B_refined | 12.472 |
r_long_range_B_other | 12.472 |
r_dihedral_angle_4_deg | 11.105 |
r_scangle_other | 10.463 |
r_mcangle_it | 7.817 |
r_mcangle_other | 7.815 |
r_scbond_it | 7.574 |
r_scbond_other | 7.409 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2577 |
Nucleic Acid Atoms | |
Solvent Atoms | 147 |
Heterogen Atoms | 55 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |