2Y43
Rad18 ubiquitin ligase RING domain structure
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 5.5 | 15% PEG 3350, 100 MM AMMONIUM ACETATE, 100 MM BIS-TRIS PH 5.5 . | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2 | 38 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 104.646 | α = 90 |
| b = 29.357 | β = 125.05 |
| c = 69.736 | 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 315r | 2009-05-17 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 | |
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 | 42.84 | 99.9 | 0.09 | 24.3 | 17.3 | 16560 | 3 | 18.4 | ||||||||||
| 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 | 1.8 | 1.89 | 99.2 | 0.62 | 2.5 | 5.8 | |||||||||||||
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | NONE | 1.8 | 42.86 | 15732 | 828 | 99.92 | 0.1774 | 0.17505 | 0.22311 | RANDOM | 22.531 | ||||||
| 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] | |
| 0.63 | 0.27 | -0.04 | -0.28 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.691 |
| r_dihedral_angle_3_deg | 13.431 |
| r_dihedral_angle_4_deg | 13.193 |
| r_dihedral_angle_1_deg | 5.122 |
| r_scangle_it | 3.252 |
| r_scbond_it | 1.931 |
| r_angle_refined_deg | 1.207 |
| r_mcangle_it | 1.08 |
| r_mcbond_it | 0.553 |
| r_chiral_restr | 0.089 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1421 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 102 |
| Heterogen Atoms | 4 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data reduction |
| SCALA | data scaling |
| SHELX | phasing |
| PHASER | phasing |
| REFMAC | refinement |
