8QAF
X-ray crystal structure of a de novo designed single-chain antiparallel 8-helix coiled-coil alpha-helical barrel, sc-apCC-8
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 0.2 M sodium formate, 0.1 M Bis Tris propane, pH 8.5, 20 % w/v PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.86 | 33.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.002 | α = 90 |
b = 50.002 | β = 90 |
c = 57.249 | γ = 90 |
Symmetry | |
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Space Group | P 4 21 2 |
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 PILATUS 6M | 2023-05-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.999 | Diamond | I24 |
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 | 37.66 | 99.62 | 0.01179 | 0.01668 | 0.01179 | 0.934 | 15.06 | 2 | 5290 | 35.05 |
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 | 2.07 | 100 | 0.09224 | 0.1305 | 0.09224 | 0.976 | 5.24 |
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 | AB INITIO PHASING | FREE R-VALUE | 2 | 37.66 | 1.36 | 5271 | 248 | 99.64 | 0.2492 | 0.2489 | 0.2524 | 41.25 |
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 | 3.2786 |
f_angle_d | 0.5725 |
f_chiral_restr | 0.0442 |
f_bond_d | 0.0063 |
f_plane_restr | 0.0035 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 367 |
Nucleic Acid Atoms | |
Solvent Atoms | 14 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
AutoProcess | data reduction |
AutoProcess | data scaling |
Arcimboldo | phasing |