2A4E
Crystal structure of mouse cadherin-11 EC1-2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZVN | PDB entry 1ZVN and 1ZXK for the EC1 domain, and the EC2 domains of PDB entries 1NCJ, 1EDH, and 1L3W, for the EC2 domain. |
experimental model | PDB | 1ZXK | PDB entry 1ZVN and 1ZXK for the EC1 domain, and the EC2 domains of PDB entries 1NCJ, 1EDH, and 1L3W, for the EC2 domain. |
experimental model | PDB | 1NCJ | PDB entry 1ZVN and 1ZXK for the EC1 domain, and the EC2 domains of PDB entries 1NCJ, 1EDH, and 1L3W, for the EC2 domain. |
experimental model | PDB | 1EDH | PDB entry 1ZVN and 1ZXK for the EC1 domain, and the EC2 domains of PDB entries 1NCJ, 1EDH, and 1L3W, for the EC2 domain. |
experimental model | PDB | 1L3W | PDB entry 1ZVN and 1ZXK for the EC1 domain, and the EC2 domains of PDB entries 1NCJ, 1EDH, and 1L3W, for the EC2 domain. |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | ammonium sulfate, hepes, sucrose, calcium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.37 | 77.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 203.249 | α = 90 |
b = 203.249 | β = 90 |
c = 42.811 | γ = 120 |
Symmetry | |
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Space Group | P 62 2 2 |
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 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.9795 | NSLS | X4A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.2 | 30 | 99.9 | 8610 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 3.2 | 3.31 | 100 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1ZVN and 1ZXK for the EC1 domain, and the EC2 domains of PDB entries 1NCJ, 1EDH, and 1L3W, for the EC2 domain. | 3.2 | 30 | 8536 | 433 | 98.56 | 0.213 | 0.211 | 0.247 | RANDOM | 74.397 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.64 | 0.32 | 0.64 | -0.96 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.984 |
r_dihedral_angle_3_deg | 23.83 |
r_dihedral_angle_4_deg | 18.619 |
r_dihedral_angle_1_deg | 7.332 |
r_scangle_it | 2.683 |
r_angle_refined_deg | 1.764 |
r_scbond_it | 1.542 |
r_mcangle_it | 1.131 |
r_mcbond_it | 0.626 |
r_nbtor_refined | 0.328 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1612 |
Nucleic Acid Atoms | |
Solvent Atoms | 15 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
CCP4 | data scaling |
PHASER | phasing |