3K6F
Crystal structure of mouse T-cadherin EC1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3K6D | PRB entry 3K6D |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 277 | 0.2M Ammonium sulfate, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.05 | 40.03 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 50.355 | α = 90 |
b = 50.355 | β = 90 |
c = 122.46 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 62 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | MAR scanner 345 mm plate | Vertical focusing mirror | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4C | 0.9791 | NSLS | X4C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.8 | 30 | 99.3 | 0.048 | 10.8 | 16137 | 17.473 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.8 | 1.9 | 99.9 | 0.125 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | 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 | PRB entry 3K6D | 1.813 | 19.447 | 15825 | 1584 | 99.43 | 0.168 | 0.168 | 0.226 | 22.144 |
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] | |
2.404 | 2.404 | -4.809 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.215 |
f_nbd_refined | 4.127 |
f_angle_d | 1.361 |
f_chiral_restr | 0.088 |
f_bond_d | 0.009 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1538 |
Nucleic Acid Atoms | |
Solvent Atoms | 203 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MAR345dtb | data collection |
DENZO | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |