8A0K
crystal structure of the kinetoplastid kinetochore protein Trypanosoma brucei KKT3 Divergent Polo-Box domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277.15 | 25% PEG3350, 0.1 M Bis-Tris pH 5.5 and 0.1 M tri-sodium acetate pH 4.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.998 | α = 84.11 |
b = 52.485 | β = 84.42 |
c = 102.152 | γ = 73.25 |
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 | PIXEL | DECTRIS PILATUS3 6M | 2016-08-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 1.0072 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.92 | 50.68 | 99 | 0.155 | 0.184 | 0.098 | 0.976 | 5.1 | 3.4 | 19067 | 63.19 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.92 | 3 | 98.4 | 1.022 | 1.213 | 0.643 | 0.53 | 3.4 |
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 | partial Se-Met model | 2.92 | 50.68 | 18988 | 952 | 98.6 | 0.2515 | 0.2504 | 0.2712 | RANDOM | 81.54 |
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] | |
6.7368 | -8.0496 | -3.4721 | 1.8403 | -23.9987 | -8.577 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 18.98 |
t_omega_torsion | 2.84 |
t_angle_deg | 1.04 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6169 |
Nucleic Acid Atoms | |
Solvent Atoms | 50 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
DIALS | data reduction |
Aimless | data scaling |
PHASER | phasing |
BUSTER | refinement |
PDB_EXTRACT | data extraction |