5YR0
Structure of Beclin1-UVRAG coiled coil domain complex
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 289 | 0.1M citric acid pH 3.5, 3.0M sodium chloride | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.05 | 39.91 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 45.112 | α = 90 |
| b = 45.112 | β = 90 |
| c = 161.524 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 61 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2012-03-30 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | ||
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 | 50 | 100 | 0.07 | 41.7 | 20 | 8323 | ||||||||||||
| 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 | 1.86 | 0.165 | 22.6 | |||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SIRAS | THROUGHOUT | 1.9 | 35.18 | 7908 | 419 | 99.55 | 0.1707 | 0.16943 | 0.19455 | RANDOM | 22.352 | |||||||
| 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] | |
| -0.04 | -0.02 | -0.04 | 0.14 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 28.278 |
| r_dihedral_angle_3_deg | 16.269 |
| r_dihedral_angle_4_deg | 13.138 |
| r_long_range_B_refined | 10.322 |
| r_long_range_B_other | 9.889 |
| r_scangle_other | 5.54 |
| r_dihedral_angle_1_deg | 3.848 |
| r_mcangle_it | 3.457 |
| r_mcangle_other | 3.454 |
| r_scbond_it | 3.441 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 767 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 164 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| SHARP | phasing |
