7FT2
SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z235449082
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 100 mM Morpheus amino acids, 100 mM Morpheus buffer system 1, 43% Morpheus precipitant mix 3 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.71 | 54.69 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 79.579 | ¦Á = 90 |
| b = 49.922 | ¦Â = 94.55 |
| c = 117.517 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 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 | 2022-04-14 | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9179 | Diamond | I04-1 |
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 | 2.04 | 117.15 | 99.9 | 0.178 | 0.211 | 0.112 | 0.99 | 7.5 | 3.5 | 59263 | |||||||||
| 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 | 2.04 | 2.09 | 98.6 | 1.466 | 1.726 | 0.905 | 0.38 | 3.6 | 4332 | ||||||||||
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 | FOURIER SYNTHESIS | THROUGHOUT | 8BLU | 2.04 | 117.15 | 56310 | 2877 | 99.68 | 0.2706 | 0.268 | 0.3215 | RANDOM | 38.381 | ||||||
| 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] | |
| -2.46 | 1.73 | -0.38 | 2.53 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.502 |
| r_dihedral_angle_3_deg | 19.017 |
| r_dihedral_angle_4_deg | 17.769 |
| r_dihedral_angle_1_deg | 7.447 |
| r_mcangle_it | 2.214 |
| r_angle_refined_deg | 1.634 |
| r_angle_other_deg | 1.267 |
| r_mcbond_it | 1.213 |
| r_mcbond_other | 1.208 |
| r_chiral_restr | 0.07 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5908 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 369 |
| Heterogen Atoms | 107 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Aimless | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| REFMAC | phasing |
