8HKR
Crystal Structure of Histone H3 Lysine 79 (H3K79) Methyltransferase Rv2067c from Mycobacterium tuberculosis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 295 | Buffer: 0.1 M imidazole/MES acid, pH 6.5: Precipitant: 20% w/v polyethylene glycol 500* monomethyl ether + 10% w/v polyethylene glycol 20,000: Additive: 0.03 M sodium nitrate + 0.03 M sodium phosphate dibasic + 0.03 M ammonium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.49 | 64.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 109.15 | α = 90 |
b = 109.15 | β = 90 |
c = 216.61 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 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 | PIXEL | DECTRIS PILATUS3 6M | 2018-12-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.699996 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.4 | 48.81 | 100 | 0.089 | 0.09 | 0.999 | 24.37 | 25.383 | 51986 | 71.257 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.4 | 2.46 | 100 | 2.223 | 2.268 | 0.741 | 1.71 | 25.633 |
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 | Determined using iodine SAD; experimental phasing | 2.4 | 48.81 | 49385 | 2600 | 99.98 | 0.2025 | 0.2017 | 0.2183 | RANDOM | 66.041 |
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] | |
0.5 | 0.5 | -1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.279 |
r_dihedral_angle_4_deg | 16.414 |
r_dihedral_angle_3_deg | 14.85 |
r_dihedral_angle_1_deg | 7.05 |
r_mcangle_it | 2.767 |
r_mcbond_it | 1.77 |
r_mcbond_other | 1.77 |
r_angle_refined_deg | 1.337 |
r_angle_other_deg | 1.19 |
r_chiral_restr | 0.059 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6068 |
Nucleic Acid Atoms | |
Solvent Atoms | 54 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
PHASER | phasing |
CRANK2 | phasing |
PDB_EXTRACT | data extraction |
XDS | data reduction |