2V66
Crystal Structure of the coiled-coil domain of Ndel1 (a.a. 58 to 169) C
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6.8 | 4% PEG 8000, 50 MM SODIUM PHOSPHATE PH 6.8, 100 MM NACL. PROTEIN CONCENTRATION 20 MG/ML. CRYOBUFFER = RESERVOIR PLUS 17% PEG 400. | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.11 | 41.32 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 46.431 | α = 90 |
| b = 73.221 | β = 105.4 |
| c = 69.026 | γ = 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 | CCD | ADSC CCD | 2005-02-24 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 | |
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 | 2.1 | 49.3 | 99.8 | 0.08 | 5 | 11.5 | 300363 | 2 | |||||||||||
| 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 | 2.1 | 2.17 | 100 | 0.31 | 2.2 | 12 | |||||||||||||
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 | MAD | THROUGHOUT | NONE | 2.1 | 18 | 24984 | 1074 | 99.9 | 0.236 | 0.233 | 0.31 | RANDOM | 30.26 | ||||||
| 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] | |
| -3.52 | -2.25 | 2.86 | -0.54 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.386 |
| r_dihedral_angle_3_deg | 19.631 |
| r_dihedral_angle_4_deg | 19.627 |
| r_dihedral_angle_1_deg | 5.731 |
| r_scangle_it | 5.335 |
| r_scbond_it | 3.486 |
| r_angle_refined_deg | 1.922 |
| r_mcangle_it | 1.836 |
| r_mcbond_it | 1.279 |
| r_symmetry_vdw_refined | 0.34 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3700 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 123 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| SHARP | phasing |
