7ZA1
GPC3-Unc5D octamer structure and role in cell migration
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5FTT | 5FTT, hGPC3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8.5 | 291.15 | 20% ethylene glycol, 10% w/v PEG 8000, 0.1 M Tris/BICINE (pH 8.5) and 0.02 M of amino acids (L-Na-glutamate, alanine, glycine, lysine-HCl, and serine) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.98 | 58.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.643 | α = 90 |
b = 157.584 | β = 102.949 |
c = 126.601 | 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 PILATUS 6M-F | 2018-09-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.91587 | Diamond | I04-1 |
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 | 4.1 | 123.4 | 73 | 0.109 | 0.13 | 0.071 | 0.994 | 3.4 | 3.4 | 22459 | 143.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 4.1 | 4.55 | 10.9 | 0.738 | 1.6 | 3.5 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5FTT, hGPC3 | 4.1 | 97.336 | 18399 | 899 | 59.546 | 0.326 | 0.3239 | 0.3648 | 186.258 |
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] | |
0.883 | 1.725 | 3.2 | -4.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.776 |
r_lrange_it | 17.238 |
r_lrange_other | 17.238 |
r_dihedral_angle_3_deg | 16.034 |
r_dihedral_angle_4_deg | 12.084 |
r_mcangle_it | 6.562 |
r_mcangle_other | 6.562 |
r_scangle_it | 5.457 |
r_scangle_other | 5.457 |
r_mcbond_it | 3.643 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19184 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 462 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
autoPROC | data reduction |
xia2 | data scaling |
PHENIX | phasing |