Protein structure determination by electron diffraction using a single three-dimensional nanocrystal
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2YBL | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 104.56 | α = 90 |
| b = 68.05 | β = 90 |
| c = 32.05 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 2 |
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-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | Mean Isotropic B | |||||||
| ELECTRON CRYSTALLOGRAPHY | MOLECULAR REPLACEMENT | NONE | 2ybl | 2.11 | 57.03 | 8503 | 8503 | 61.24 | 0.264 | 0.283 | 0.279 | 26.968 | |||||||
| 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] | |
| -0.67 | 0.96 | -0.29 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.709 |
| r_dihedral_angle_4_deg | 17.395 |
| r_dihedral_angle_3_deg | 16.684 |
| r_dihedral_angle_1_deg | 6.491 |
| r_long_range_B_refined | 6.356 |
| r_long_range_B_other | 6.356 |
| r_scangle_other | 3.19 |
| r_mcangle_other | 2.557 |
| r_mcangle_it | 2.556 |
| r_scbond_it | 1.937 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Sample |
|---|
| Lysozyme C |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 3D ARRAY |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | CRYSTALLOGRAPHY |
| Number of Particles | |
| Reported Resolution (Å) | |
| Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
| Other Details | |
| Refinement Type | |
| Symmetry Type | 3D CRYSTAL |
| Space Group Name | |
| Length a | 104.56 |
| Length b | 68.05 |
| Length c | 68.05 |
| Angle Alpha | 90 |
| Angle Beta | 90 |
| Angle Gamma | 90 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | |||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | OTHER | ||||||||
| Electron Dose (electrons/Å**2) | 0.04 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | DIFFRACTION |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
