3LND
Crystal structure of cadherin-6 EC12 W4A
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 293 | 0.1M HEPES pH 7.5, 17% (v/v) isopropanol, 12% (w/v) PEG 4000, 9mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.979 | α = 90 |
b = 113.555 | β = 96.01 |
c = 67.907 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 4 | 2008-04-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | NSLS | X4A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.82 | 50 | 98.4 | 0.088 | 12.9 | 3.3 | 20165 | 1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.82 | 20 | 20529 | 19102 | 1021 | 98.9 | 0.211 | 0.207 | 0.282 | RANDOM | 58.62 |
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] | |
4.27 | 1.08 | -2.51 | -1.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.677 |
r_dihedral_angle_4_deg | 19.36 |
r_dihedral_angle_3_deg | 17.546 |
r_dihedral_angle_1_deg | 5.921 |
r_angle_refined_deg | 1.051 |
r_scangle_it | 0.785 |
r_scbond_it | 0.489 |
r_mcangle_it | 0.401 |
r_nbtor_refined | 0.3 |
r_mcbond_it | 0.227 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6229 |
Nucleic Acid Atoms | |
Solvent Atoms | 149 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
MOLREP | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |