7YHL
Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with free phosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 298 | 0.1 M Sodium acetate trihydrate, pH 4.5, 25% w/v Polyethylene glycol 1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.027 | α = 90 |
b = 38.376 | β = 106.412 |
c = 69.798 | 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 | 2022-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL02U1 | 0.97919 | 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 | 2.7 | 40.95 | 95.55 | 0.067 | 0.998 | 10.9 | 5.29 | 9099 |
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 | 2.7 | 2.79 | 95.55 | 0.748 | 0.805 | 1.5 | 5.32 |
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 (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.7 | 40.95 | 9098 | 483 | 93.862 | 0.264 | 0.2631 | 0.2877 | 117.165 |
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] | |
2.966 | 2.857 | -2.26 | -2.036 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_lrange_it | 28.921 |
r_lrange_other | 28.921 |
r_scangle_other | 19.069 |
r_scangle_it | 19.041 |
r_mcangle_it | 18.559 |
r_mcangle_other | 18.553 |
r_dihedral_angle_3_deg | 16.973 |
r_dihedral_angle_6_deg | 15.479 |
r_mcbond_it | 12.983 |
r_mcbond_other | 12.98 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2697 |
Nucleic Acid Atoms | |
Solvent Atoms | 3 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data scaling |
MOLREP | phasing |
PHENIX | model building |
Coot | model building |
XDS | data reduction |