Crystal structure of the 2nd SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide (aa 76-91) from human ARAP1
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | 0.1 M HEPES pH 7.5, 1.4 M tri-sodium citrate dehydrate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.74 | 29.19 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 44.59 | α = 90 |
| b = 44.59 | β = 90 |
| c = 32.94 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 |
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 | PSI PILATUS 6M | 2013-11-10 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97625 | Diamond | I04 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.58 | 44.59 | 99.9 | 2.24 | 7.2 | 8587 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | THROUGHOUT | 1.58 | 44.59 | 8587 | 432 | 99.89 | 0.16154 | 0.15966 | 0.17 | 0.19993 | 0.21 | RANDOM | 22.071 | ||||||
| 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] | |
| -0.3 | -0.3 | 0.61 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.181 |
| r_dihedral_angle_4_deg | 23.369 |
| r_dihedral_angle_3_deg | 14.214 |
| r_long_range_B_refined | 7.033 |
| r_long_range_B_other | 6.943 |
| r_dihedral_angle_1_deg | 6.201 |
| r_scangle_other | 4.833 |
| r_mcangle_other | 4.058 |
| r_mcangle_it | 4.057 |
| r_scbond_it | 3.332 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 578 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 68 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SCALA | data scaling |
| MOSFLM | data reduction |
| PHASER | phasing |
