6EQS
Human Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RIY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | 30% PEG3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, 5% 1,3-butandiol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.326 | α = 97.39 |
b = 55.969 | β = 99.29 |
c = 123.034 | γ = 90.52 |
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 PILATUS 2M-F | 2016-12-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.000030 | SLS | X06DA |
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 | 1.32 | 43.77 | 91.5 | 0.059 | 0.999 | 6.8 | 2 | 227669 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.32 | 1.4 | 88.1 | 0.959 | 0.723 | 1.1 | 1.9 |
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 | 3RIY | 1.32 | 43.77 | 224952 | 2388 | 91.87 | 0.16076 | 0.16025 | 0.20856 | RANDOM | 21.373 |
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] | |
-2.34 | 3.38 | -2.91 | -1.76 | 0.81 | 4.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 47.72 |
r_dihedral_angle_2_deg | 34.612 |
r_dihedral_angle_4_deg | 20.43 |
r_sphericity_bonded | 19.296 |
r_dihedral_angle_3_deg | 13.724 |
r_long_range_B_refined | 9.451 |
r_long_range_B_other | 9.451 |
r_mcangle_it | 8.762 |
r_mcangle_other | 8.762 |
r_scangle_other | 7.766 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8313 |
Nucleic Acid Atoms | |
Solvent Atoms | 1086 |
Heterogen Atoms | 440 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |