7JGZ
Protocadherin gammaC4 EC1-4 crystal structure
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 293 | 10% (w/v) PEG8000, 20% ethylene glycol, 10% Morpheus Amino Acids (Molecular Dimensions), and 0.1 M Morpheus Buffer System 2 (Hepes/MOPS buffer) pH 7.5 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
4.5 | 72.67 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 75.22 | α = 90 |
b = 115.68 | β = 90 |
c = 194.48 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2017-02-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.979180 | APS | 24-ID-E |
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 | 3.5 | 40 | 67.6 | 0.215 | 0.232 | 0.086 | 0.997 | 8.3 | 7.1 | 7545 | 77.57 |
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 | 3.5 | 3.84 | 12.5 | 0.83 | 0.896 | 0.335 | 0.829 | 2.9 | 7.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | THROUGHOUT | 4ZPO | 3.51 | 38.5 | 1.36 | 7545 | 377 | 68.53 | 0.2257 | 0.2234 | 0.271 | 101.24 |
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 | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 10.6106 |
f_angle_d | 0.8889 |
f_chiral_restr | 0.0499 |
f_plane_restr | 0.0056 |
f_bond_d | 0.0039 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3120 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 122 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |