7YR9
Crystal structure of the immature form of TtPetA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 1.6 M AmS, 20% glycerol, 0.1 M Na-Ac pH 4.6 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.51 | 50.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 32.596 | α = 90 |
b = 98.711 | β = 90.03 |
c = 51.052 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 15 | PIXEL | DECTRIS EIGER X 16M | 2020-07-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.2825 | SPring-8 | BL41XU |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.7 | 50 | 95.7 | 0.078 | 0.084 | 0.999 | 15.94 | 7.09 | 34104 | 21.741 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.7 | 1.8 | 92.5 | 0.303 | 0.327 | 0.964 | 4.72 | 7.004 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.7 | 50 | 2885 | 34104 | 1655 | 91.7 | 0.2037 | 0.2341 | 15.9042 |
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] | |
-3.693 | 1.893 | 6.066 | -2.374 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_scangle_it | 2.455 |
c_scbond_it | 1.702 |
c_mcangle_it | 1.431 |
c_mcbond_it | 0.948 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2272 |
Nucleic Acid Atoms | |
Solvent Atoms | 145 |
Heterogen Atoms | 48 |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data scaling |
SOLVE | phasing |
DM | phasing |
CNS | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |