5A3A
Crystal structure of the ADP-ribosylating sirtuin (SirTM) from Streptococcus pyogenes (Apo form)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8 | 0.1 M AMINO ACIDS, 0.1 M BUFFER SYSTEM 1 (PH 6.5), 30.00% (V/V) EDO_P8K (THESE ARE COMPONENTS OF THE MORPHEUS SCREEN FROM MOLECULAR DIMENSIONS) | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.14 | 43.44 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 34.16 | α = 99.87 |
| b = 41.51 | β = 94.63 |
| c = 51.23 | γ = 90.77 |
| Symmetry | |
|---|---|
| Space Group | P 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 | PIXEL | DECTRIS PILATUS 2M | TORROIDAL MIRROR | 2014-08-07 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | Diamond | I04-1 | |
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 | 1.54 | 34.81 | 88.3 | 0.06 | 10.6 | 3.8 | 36095 | ||||||||||||
| 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 | 1.54 | 1.58 | 82.8 | 0.55 | 2 | 3.8 | |||||||||||||
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 | 1.54 | 34.81 | 34287 | 1808 | 88.28 | 0.15205 | 0.14956 | 0.19998 | RANDOM | 19.183 | ||||||
| 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] | |
| -0.05 | -0.39 | -0.57 | 0.95 | -0.04 | -0.73 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.581 |
| r_dihedral_angle_3_deg | 13.765 |
| r_dihedral_angle_4_deg | 13.279 |
| r_dihedral_angle_1_deg | 6.183 |
| r_scangle_it | 3.595 |
| r_mcangle_it | 2.307 |
| r_scbond_it | 2.265 |
| r_mcbond_it | 1.593 |
| r_mcbond_other | 1.506 |
| r_angle_refined_deg | 1.421 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2345 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 286 |
| Heterogen Atoms | 54 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| autoSHARP | phasing |
