6RLC
Crystal structure of the PDZ tandem of syntenin in complex with fragment F13
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 277 | 100 mM Sodium Acetate pH 4.6, 200mM Ammonium Acetate, 22% PEG 3350 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.22 | 44.61 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 29.23 | α = 93.99 |
| b = 57.512 | β = 96.08 |
| c = 101.094 | γ = 107.7 |
| 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 PILATUS3 6M | 2017-11-19 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.9763 | ESRF | ID30B |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.2 | 50.02 | 96.78 | 0.069 | 0.08199 | 0.04369 | 0.997 | 9.74 | 3.5 | 106108 | 30520 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.2 | 2.279 | 95.92 | 0.3676 | 0.4347 | 0.2293 | 0.925 | 3.02 | 3.5 | 10728 | |||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.2 | 50.02 | 29031 | 1497 | 96.89 | 0.26105 | 0.25901 | 0.30141 | RANDOM | 46.873 | |||||||
| 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] | |
| 1.07 | 0.04 | 0.36 | 1.05 | -1.02 | -2.01 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.186 |
| r_dihedral_angle_4_deg | 23.972 |
| r_dihedral_angle_3_deg | 16.652 |
| r_dihedral_angle_1_deg | 7.052 |
| r_long_range_B_refined | 5.37 |
| r_long_range_B_other | 5.37 |
| r_scangle_other | 1.787 |
| r_angle_refined_deg | 1.652 |
| r_mcangle_it | 1.569 |
| r_mcangle_other | 1.564 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4949 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 148 |
| Heterogen Atoms | 92 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
