8TH6
Crystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3Q90 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277.15 | 0.1 M HEPES pH 7.5, 25% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.39 | α = 90 |
b = 78.38 | β = 108.63 |
c = 73.41 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 6M | 2020-06-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL18U1 | 0.97915 | SSRF | BL18U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.34 | 45.21 | 63.1 | 0.918 | 9.2 | 3.3 | 15966 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.34 | 2.42 | 0.848 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.34 | 45.2 | 15966 | 817 | 63.12 | 0.21698 | 0.21277 | 0.29535 | RANDOM | 26.777 |
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] | |
-0.05 | 0.05 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 17 |
r_dihedral_angle_2_deg | 13.931 |
r_dihedral_angle_1_deg | 7.326 |
r_long_range_B_refined | 5.416 |
r_long_range_B_other | 5.4 |
r_mcangle_it | 3.253 |
r_mcangle_other | 3.252 |
r_scangle_other | 2.654 |
r_mcbond_it | 1.915 |
r_mcbond_other | 1.915 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4862 |
Nucleic Acid Atoms | |
Solvent Atoms | 68 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
DIALS | data scaling |
PHASER | phasing |