2AT9
STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM BY ELECTRON CRYSTALLOGRAPHY
ELECTRON CRYSTALLOGRAPHY
Crystallization
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.2 | 71 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 62.45 | α = 90 |
| b = 62.45 | β = 90 |
| c = 100 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 3 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | |||||||||||||
Data Collection
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| ELECTRON CRYSTALLOGRAPHY | THROUGHOUT | 3 | 8 | 1 | 6107 | 358 | 73.7 | 0.237 | 0.237 | 0.33 | RANDOM | 14.2 | |||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| x_dihedral_angle_d | 25.9 |
| x_angle_deg | 1.7 |
| x_improper_angle_d | 1 |
| x_bond_d | 0.013 |
| x_bond_d_na | |
| x_bond_d_prot | |
| x_angle_d | |
| x_angle_d_na | |
| x_angle_d_prot | |
| x_angle_deg_na | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1721 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 2 |
| Heterogen Atoms | 500 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| X-PLOR | model building |
| X-PLOR | refinement |
| X-PLOR | phasing |
| Sample |
|---|
| Bacteriorhodopsin |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 2D ARRAY |
| Embedding Material | trehalose |
| Embedding Details | 3% (w/v) trehalose |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | CRYSTALLOGRAPHY |
| Number of Particles | |
| Reported Resolution (Å) | 3 |
| Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
| Other Details | |
| Refinement Type | |
| Symmetry Type | |
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GENERIC GATAN | KODAK SO-163 FILM | |||||||
| Electron Dose (electrons/Å**2) | 10 | 30 | |||||||
| Imaging Experiment | 1 | 2 |
|---|---|---|
| Date of Experiment | ||
| Temperature (Kelvin) | ||
| Microscope Model | JEOL 4000 | JEOL 3000SFF |
| Minimum Defocus (nm) | ||
| Maximum Defocus (nm) | ||
| Minimum Tilt Angle (degrees) | ||
| Maximum Tilt Angle (degrees) | ||
| Nominal CS | ||
| Imaging Mode | DIFFRACTION | BRIGHT FIELD |
| Specimen Holder Model | ||
| Nominal Magnification | ||
| Calibrated Magnification | ||
| Source | FIELD EMISSION GUN | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | ||
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| CRYSTALLOGRAPHY MERGING | LATLINE | |
| CRYSTALLOGRAPHY MERGING | CCP4 package | |
| OTHER | MRC package | |
| MODEL FITTING | O | |
| MODEL REFINEMENT | X-PLOR | |
