7NFN
A heptameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-L21N-I24N.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 292 | After 1:1 dilution with the peptide solution, the resulting conditions were 100 mM magnesium chloride hexahydrate, 50 mM 2-amino-2-(hydroxymethyl)propane-1,3-diol (TRIS) and 1.7 M 1,6-hexanediol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.898 | α = 67.39 |
b = 47.91 | β = 67.49 |
c = 62.277 | γ = 77.73 |
Symmetry | |
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Space Group | P 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 XE 16M | 2019-10-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
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 | 1.45 | 44.16 | 95.9 | 0.051 | 0.06 | 0.032 | 0.998 | 10.6 | 3.5 | 79988 | 16.22 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.45 | 1.47 | 86.6 | 0.643 | 0.783 | 0.44 | 0.715 | 1.6 | 3 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | model helices | 1.45 | 44.16 | 75966 | 3975 | 95.81 | 0.1359 | 0.1338 | 0.1777 | RANDOM | 21.324 |
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] | |
0.75 | 0.45 | -0.01 | 1.51 | -0.65 | -1.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.189 |
r_dihedral_angle_4_deg | 13.356 |
r_dihedral_angle_3_deg | 13.126 |
r_dihedral_angle_1_deg | 3.726 |
r_rigid_bond_restr | 2.988 |
r_angle_refined_deg | 1.666 |
r_angle_other_deg | 1.595 |
r_chiral_restr | 0.098 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3232 |
Nucleic Acid Atoms | |
Solvent Atoms | 378 |
Heterogen Atoms | 56 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DIALS | data reduction |
Aimless | data scaling |
xia2 | data scaling |
PHASER | phasing |