2QKU
The 5th PDZ Domain of InaD in 10mM DTT
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | 1.3M Na Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.16 | 61.14 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 67.7 | α = 90 |
| b = 67.7 | β = 90 |
| c = 162.5 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2000-03-18 | M | MAD | ||||||
| 2 | 1 | x-ray | 100 | M | ||||||||||
| 3 | 1 | x-ray | 100 | M | ||||||||||
| 4 | 1 | x-ray | 100 | M | ||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL1-5 | .97965 | SSRL | BL1-5 |
| 2 | SYNCHROTRON | SSRL BEAMLINE BL1-5 | .980035 | SSRL | BL1-5 |
| 3 | SYNCHROTRON | SSRL BEAMLINE BL1-5 | .925256 | SSRL | BL1-5 |
| 4 | SYNCHROTRON | SSRL BEAMLINE BL1-5 | 1.06883 | SSRL | BL1-5 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | ||||||||
| 1,2,3,4 | 2.2 | 40 | 97.9 | 0.116 | 10.4 | 35921 | 14.5 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1,2,3,4 | 2.2 | 2.41 | 96 | 0.553 | 2.1 | ||||||||||||||
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 | MAD | THROUGHOUT | 2.2 | 29.77 | 33753 | 1700 | 92.1 | 0.206 | 0.206 | 0.231 | RANDOM | 24 | |||||||
| 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] | |
| 1.5 | 1.5 | -3 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 25.9 |
| c_scangle_it | 3.46 |
| c_scbond_it | 2.43 |
| c_mcangle_it | 2 |
| c_angle_deg | 1.3 |
| c_mcbond_it | 1.28 |
| c_improper_angle_d | 0.72 |
| c_bond_d | 0.006 |
| c_bond_d_na | |
| c_bond_d_prot | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1973 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 266 |
| Heterogen Atoms | 12 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
