3AX5
Crystal structure of rat TOM20-ALDH presequence complex: A complex (form1) between Tom20 and a disulfide-bridged presequence peptide containing D-Cys and L-Cys at the i and i+3 positions.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 0.1M HEPES-NaOH pH7.0, 10% isopropanol, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.53 | 51.37 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 41.745 | α = 90 |
| b = 77.401 | β = 90 |
| c = 116.226 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 2 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 | 95 | CCD | ADSC QUANTUM 315r | 2010-10-29 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | |||||||||||||
| 3 | 1 | |||||||||||||
| 4 | 1 | |||||||||||||
| 5 | 1 | |||||||||||||
| 6 | 1 | |||||||||||||
| 7 | 1 | |||||||||||||
| 8 | 1 | |||||||||||||
| 9 | 1 | |||||||||||||
| 10 | 1 | |||||||||||||
| 11 | 1 | |||||||||||||
| 12 | 1 | |||||||||||||
| 13 | 1 | |||||||||||||
| 14 | 1 | |||||||||||||
| 15 | 1 | |||||||||||||
| 16 | 1 | |||||||||||||
| 17 | 1 | |||||||||||||
| 18 | 1 | |||||||||||||
| 19 | 1 | |||||||||||||
| 20 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 0.98 | Photon Factory | BL-17A |
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 | 2.2 | 30 | 99.9 | 0.101 | 15.924 | 7.1 | 9917 | ||||||||||||
| 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 | 2.2 | 2.24 | 100 | 0.561 | 7.2 | 476 | |||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1WT4 | 2.2 | 28.4 | 9438 | 477 | 99.74 | 0.22473 | 0.22209 | 0.27554 | RANDOM | 38.74 | ||||||
| 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] | |
| 0.19 | -0.11 | -0.08 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.987 |
| r_dihedral_angle_4_deg | 25.402 |
| r_dihedral_angle_3_deg | 19.706 |
| r_scangle_it | 5.974 |
| r_dihedral_angle_1_deg | 5.7 |
| r_scbond_it | 3.536 |
| r_mcangle_it | 2.223 |
| r_angle_refined_deg | 1.902 |
| r_mcbond_it | 1.14 |
| r_chiral_restr | 0.131 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1266 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 23 |
| Heterogen Atoms | 5 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
