3LNI
Crystal structure of E-cadherin EC12 E89A
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 0.25M ammonium sulfate, 0.1M MES pH 6.5, 26% PEG 5000 monomethylether, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.22 | 61.83 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 119.63 | α = 90 |
| b = 77.122 | β = 115.25 |
| c = 71.675 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 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 | 2007-03-17 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.9795 | NSLS | X4A |
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 | 2.3 | 50 | 99 | 0.093 | 11.8 | 3 | 28461 | 28177 | 1 | 1 | |||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1EDH | 2.3 | 20 | 28177 | 26309 | 1387 | 98.75 | 0.169 | 0.1689 | 0.16578 | 0.22753 | RANDOM | 34.417 | ||||
| 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] | |
| 1.4 | 2.45 | -0.19 | 0.88 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.189 |
| r_dihedral_angle_4_deg | 16.773 |
| r_dihedral_angle_3_deg | 14.332 |
| r_dihedral_angle_1_deg | 6.583 |
| r_scangle_it | 2.967 |
| r_scbond_it | 1.8 |
| r_angle_refined_deg | 1.48 |
| r_mcangle_it | 1.037 |
| r_mcbond_it | 0.644 |
| r_nbtor_refined | 0.301 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3194 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 564 |
| Heterogen Atoms | 6 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| ADSC | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
