4UXJ
Leishmania major Thymidine Kinase in complex with dTTP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 8 | 50 MM HEPES PH 8.0, 36% (W/V) PENTA-ERYTHRITOL-PROPOXYLATE, 1 MM DTTP, 3 MM MGCL2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.7 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 61.6 | ¦Á = 81.07 |
b = 61.63 | ¦Â = 85.8 |
c = 110.09 | ¦Ã = 74.94 |
Symmetry | |
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Space Group | P 1 |
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 | ADSC CCD | 2013-02-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
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 | 3 | 59.54 | 94.7 | 0.14 | 6.2 | 2 | 29290 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3 | 3.16 | 94.7 | 0.6 | 2.1 | 2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 3 | 108.69 | 27884 | 1404 | 94.7 | 0.26118 | 0.2603 | 0.27837 | RANDOM | 45.128 |
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] | |
-0.26 | 1.01 | -2.72 | -0.39 | -0.69 | 0.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.447 |
r_dihedral_angle_3_deg | 15.625 |
r_dihedral_angle_4_deg | 13.882 |
r_dihedral_angle_1_deg | 5.904 |
r_long_range_B_refined | 4.957 |
r_long_range_B_other | 4.94 |
r_scangle_other | 2.757 |
r_mcangle_it | 2.417 |
r_mcangle_other | 2.416 |
r_scbond_it | 1.94 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9673 |
Nucleic Acid Atoms | |
Solvent Atoms | 53 |
Heterogen Atoms | 232 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |