5Y2F
Human SIRT6 in complex with allosteric activator MDL-801
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291.15 | 0.2 M (NH4)2SO4, 0.1 M Mes pH 6.5, 20% W/v PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.97 | 72.47 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 162.422 | ¦Á = 90 |
b = 162.422 | ¦Â = 90 |
c = 162.422 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 41 3 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 | CCD | RAYONIX MX-300 | 2016-08-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97857 | APS | 21-ID-F |
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 | 2.53 | 114.85 | 98.7 | 0.137 | 30.8 | 42.7 | 24828 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.53 | 2.66 | 100 | 41.9 |
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 | THROUGHOUT | 2.53 | 114.85 | 23520 | 1261 | 98.71 | 0.17724 | 0.17505 | 0.21664 | RANDOM | 69.863 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.347 |
r_dihedral_angle_4_deg | 18.681 |
r_dihedral_angle_3_deg | 14.924 |
r_long_range_B_other | 13.005 |
r_long_range_B_refined | 12.941 |
r_scangle_other | 8.344 |
r_mcangle_it | 6.958 |
r_mcangle_other | 6.958 |
r_dihedral_angle_1_deg | 5.846 |
r_scbond_it | 5.217 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2368 |
Nucleic Acid Atoms | |
Solvent Atoms | 132 |
Heterogen Atoms | 158 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data processing |
Aimless | data scaling |
PHASER | phasing |