Crystal Structure of SecYE translocon from Thermus thermophilus with a Fab fragment
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 11% PEG 1500, 0.1M HEPES-Na (pH 7.5), 0.14M ammonium formate, 0.02% n-Dodecyl-beta-D-maltoside, 0.002M zinc acetate, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.59 | 65.72 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 189.096 | α = 90 |
| b = 103.073 | β = 105.18 |
| c = 78.005 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 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 QUANTUM 315 | 2007-10-04 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2006-10-25 | M | MAD | ||||||
| 1,2 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 0.97942 | SPring-8 | BL41XU |
| 2 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 0.97920,0.97942,0.96418 | Photon Factory | AR-NW12A |
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 | |||||||||
| 1,2 | 3.2 | 48.43 | 22585 | ||||||||||||||||
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 | MAD | THROUGHOUT | 3.2 | 48.43 | 22465 | 1212 | 98.62 | 0.24604 | 0.24424 | 0.26 | 0.2798 | 0.25 | RANDOM | 127.5 | |||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| -4.64 | 3.82 | 1.58 | 5.06 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.62 |
| r_dihedral_angle_4_deg | 21.039 |
| r_dihedral_angle_3_deg | 19.415 |
| r_dihedral_angle_1_deg | 6.1 |
| r_angle_refined_deg | 1.148 |
| r_scangle_it | 0.899 |
| r_mcangle_it | 0.636 |
| r_scbond_it | 0.514 |
| r_mcbond_it | 0.353 |
| r_nbtor_refined | 0.309 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6930 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CNS | refinement |
| ADSC | data collection |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| SHARP | phasing |
| REFMAC | refinement |
