5A3B
Crystal structure of the ADP-ribosylating sirtuin (SirTM) from Streptococcus pyogenes in complex with ADP-ribose
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8 | CRYSTALLIZATION CONDITIONS: 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 = 33.943 | α = 99.76 |
| b = 41.521 | β = 93.4 |
| c = 51.253 | γ = 92.66 |
| 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 6M | MIRRORS | 2014-08-03 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 | |
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 | 1.9 | 29.35 | 92.1 | 0.07 | 8 | 2.4 | 19940 | ||||||||||||
| 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 | 1.9 | 1.94 | 88.9 | 0.33 | 4.5 | 2.2 | |||||||||||||
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 | 1.9 | 50.39 | 18929 | 1010 | 92.08 | 0.16586 | 0.16318 | 0.21577 | RANDOM | 14.412 | ||||||
| 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] | |
| -0.32 | -0.14 | -0.19 | 0.55 | 0.36 | -0.29 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.771 |
| r_dihedral_angle_3_deg | 13.459 |
| r_dihedral_angle_4_deg | 12.946 |
| r_dihedral_angle_1_deg | 5.399 |
| r_scangle_it | 2.51 |
| r_mcangle_it | 1.809 |
| r_scbond_it | 1.476 |
| r_angle_refined_deg | 1.446 |
| r_mcbond_it | 1.073 |
| r_mcbond_other | 1.073 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2345 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 248 |
| Heterogen Atoms | 57 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| autoSHARP | phasing |
