4DG6
Crystal structure of domains 1 and 2 of LRP6
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | hanging drop | 5.9 | 292 | 20% PEG 8000, 20mM ammonium sulfate, pH 5.9, hanging drop, temperature 292K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.25 | 62.1 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 109.36 | α = 90 |
| b = 109.36 | β = 90 |
| c = 130.88 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 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 315r | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9795 | Diamond | I04-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.88 | 32.72 | 99.6 | 0.052 | 25 | 7.3 | 21004 | 21004 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2.88 | 2.95 | 99.9 | 0.708 | 0.708 | 1.1 | 7.5 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | 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 | 2.9 | 32.09 | 20470 | 2009 | 99.7 | 0.257 | 0.257 | 0.313 | 74.12 | |||||||||
| 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] | |
| -11.907 | -16.741 | -11.907 | 23.813 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_mcangle_it | 1.798 |
| c_scangle_it | 1.695 |
| c_scbond_it | 0.991 |
| c_mcbond_it | 0.989 |
| c_bond_d | 0.009 |
| c_bond_d_na | |
| c_bond_d_prot | |
| c_angle_d | |
| c_angle_d_na | |
| c_angle_d_prot | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4898 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 13 |
| Heterogen Atoms | 94 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALA | data scaling |
| PHASER | phasing |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
