7V0C
Structure of Ternary Complex of cGAS with dsDNA and Bound 5 -pppG(2 ,5 )pG
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4LEZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277.15 | 0.2 M ammonium acetate, 32% MPD, with 0.1 M Bis-Tris pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.08 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 78.193 | ¦Á = 90 |
b = 98.831 | ¦Â = 90 |
c = 142.619 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 EIGER X 16M | 2021-10-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-2 | 0.979338 | NSLS-II | 17-ID-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 2.56 | 29.99 | 98.9 | 0.08 | 0.087 | 0.034 | 0.999 | 13.9 | 6.6 | 35871 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.56 | 2.68 | 91.3 | 0.687 | 0.745 | 0.285 | 0.837 | 6.5 |
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 | 4lez | 2.57 | 29.99 | 34005 | 1727 | 99.07 | 0.2061 | 0.2044 | 0.2402 | RANDOM | 67.712 |
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] | |
0.28 | -0.11 | -0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.912 |
r_dihedral_angle_4_deg | 16.826 |
r_dihedral_angle_3_deg | 14.055 |
r_dihedral_angle_1_deg | 5.817 |
r_angle_refined_deg | 1.215 |
r_angle_other_deg | 1.086 |
r_chiral_restr | 0.066 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5737 |
Nucleic Acid Atoms | 1464 |
Solvent Atoms | 40 |
Heterogen Atoms | 116 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Coot | model building |
REFMAC | refinement |
PDB-REDO | refinement |
PDB_EXTRACT | data extraction |