9F5Q
Crystal structure of selenomethionine-labelled kinetoplastid kinetochore protein KKT23 acetyltransferase domain from Trypanosoma brucei
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 20% v/v jeffamine M-2070, 20% v/v DMSO |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.299 | α = 100.54 |
b = 44.528 | β = 103.17 |
c = 68.969 | γ = 101.33 |
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 | 277 | PIXEL | DECTRIS EIGER2 XE 16M | 2020-12-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9786 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 1.95 | 29.53 | 96.5 | 0.11 | 1 | 10.4 | 3.6 | 32753 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.95 | 2 | 0.704 | 0.8 | 2 |
Refinement
Statistics | |||||||||||||||||||
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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 | SAD | THROUGHOUT | 1.95 | 29.53 | 31137 | 1614 | 96.62 | 0.19982 | 0.19849 | 0.2265 | RANDOM | 29.002 |
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] | |
-1.47 | -0.89 | -0.13 | 2.68 | -0.54 | -0.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 16.125 |
r_dihedral_angle_3_deg | 13.441 |
r_long_range_B_refined | 7.749 |
r_long_range_B_other | 7.734 |
r_dihedral_angle_1_deg | 6.986 |
r_scangle_other | 6.221 |
r_scbond_it | 4.545 |
r_scbond_other | 4.498 |
r_mcangle_it | 4.069 |
r_mcangle_other | 4.068 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3455 |
Nucleic Acid Atoms | |
Solvent Atoms | 175 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
CRANK2 | phasing |