7YGH
Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with cyclic-tetraadenylate (cA4)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7YHL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 298 | 0.1 M Sodium acetate trihydrate, pH 5.0, 22% w/v Polyethylene glycol monomethyl ether 550, 5% w/v n-Dodecyl-B-D-maltoside |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.052 | α = 90 |
b = 38.837 | β = 105.798 |
c = 72.965 | 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 EIGER2 S 9M | 2022-03-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL02U1 | 0.97918 | SSRF | BL02U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 3.11 | 50 | 99.57 | 0.07 | 0.997 | 22.84 | 3.7 | 6715 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.11 | 3.22 | 100 | 0.786 | 0.602 | 1.88 |
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 (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 7YHL | 3.11 | 28.556 | 6710 | 328 | 99.54 | 0.239 | 0.2379 | 0.2584 | RANDOM | 136.267 |
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] | |
-1.611 | 3.216 | -0.998 | 0.681 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_lrange_it | 38.41 |
r_lrange_other | 38.409 |
r_mcangle_it | 30.398 |
r_mcangle_other | 30.391 |
r_scangle_it | 29.122 |
r_scangle_other | 29.116 |
r_mcbond_it | 21.768 |
r_mcbond_other | 21.768 |
r_scbond_it | 19.825 |
r_scbond_other | 19.821 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2850 |
Nucleic Acid Atoms | 88 |
Solvent Atoms | 1 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
MOLREP | phasing |
Coot | model building |
PHENIX | model building |
HKL-2000 | data reduction |