8PRL
The structure of v22Bagel8
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 5 | 293.15 | 0.1 M Citric acid pH 4.0, 20% (w/v) PEG 6000 (final pH 5.0) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.447 | α = 90 |
b = 56.447 | β = 90 |
c = 113.052 | γ = 90 |
Symmetry | |
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Space Group | P 42 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2022-08-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 1.000010 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.65 | 28.26 | 99.8 | 0.208 | 0.213 | 0.044 | 0.995 | 10.4 | 22.8 | 5777 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.65 | 2.78 | 99.2 | 0.814 | 0.837 | 0.188 | 0.922 | 17.8 |
Refinement
Statistics | |||||||||||||||||||
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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-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.65 | 28.26 | 1.34 | 5727 | 300 | 99.51 | 0.2879 | 0.2834 | 0.3702 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 7.342 |
f_angle_d | 1.007 |
f_chiral_restr | 0.058 |
f_bond_d | 0.009 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1240 |
Nucleic Acid Atoms | |
Solvent Atoms | 26 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
XDS | data reduction |
MOLREP | phasing |