Crystal structure of human cytoplasmic dynein 2 motor domain in complex with ADP.Vi
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 292 | mixing equal volumes of protein (8mg/ml) and reservoir solution (4-6 % PEG 6000 and 0.1 M Tris pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 5.83 | 78.89 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 136.03 | α = 90 |
| b = 487.15 | β = 90 |
| c = 276.46 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 21 |
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 | 2014-02-20 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | Diamond | I02 | |
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 | 3.4 | 56.5 | 62.2 | 0.101 | 7.6 | 4.1 | 78411 | ||||||||||||
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 | MIRAS | THROUGHOUT | 3.41 | 56.6 | 74060 | 3915 | 62.16 | 0.23989 | 0.23746 | 0.24 | 0.28546 | 0.28 | RANDOM | 114.274 | |||||
| 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] | |
| 0.05 | -0.28 | 0.23 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.234 |
| r_long_range_B_refined | 25.39 |
| r_long_range_B_other | 25.39 |
| r_dihedral_angle_3_deg | 17.385 |
| r_dihedral_angle_4_deg | 15.7 |
| r_scangle_other | 14.656 |
| r_mcangle_it | 13.706 |
| r_mcangle_other | 13.677 |
| r_scbond_it | 8.508 |
| r_scbond_other | 8.493 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 22697 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 119 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHARP | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
