5SZO
Protocadherin Gamma B7 extracellular cadherin domains 1-4 P41212 crystal form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4ZPL | 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN |
experimental model | PDB | 4ZPM | 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN |
experimental model | PDB | 4ZPO | 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN |
experimental model | PDB | 4ZPS | 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN |
experimental model | PDB | 5DZV | 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN |
experimental model | PDB | 5DZX | 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN |
experimental model | PDB | 4ZI9 | 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN |
experimental model | PDB | 4ZI8 | 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN |
experimental model | PDB | 5ZSM | 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN |
experimental model | PDB | 5SZN | 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 8.5 | 295 | 0.1 M Tris-Cl pH 8.5, 0.2 M trimethylamine N-oxide, 3% dextran sulfate sodium salt 5000, 17% (w/v) PEG2000MME |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.9 | 68.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.15 | α = 90 |
b = 97.15 | β = 90 |
c = 312.39 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 PILATUS 6M-F | 2015-10-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97930 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 3.59 | 104.13 | 99.6 | 0.183 | 1 | 9 | 12.5 | 18347 | 109.88 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.59 | 3.93 | 98.7 | 3.722 | 0.741 | 1 | 12.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 4ZPL, 4ZPM, 4ZPO, 4ZPS, 5DZV, 5DZX, 4ZI9, 4ZI8, 5ZSM, and 5SZN | 3.612 | 19.93 | 1.36 | 11902 | 576 | 66.6 | 0.244 | 0.2421 | 0.2787 |
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 | 13.268 |
f_angle_d | 0.588 |
f_chiral_restr | 0.042 |
f_plane_restr | 0.004 |
f_bond_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6164 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 129 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |