ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5KXV | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 66.92 | α = 90 |
| b = 66.92 | β = 90 |
| c = 107.56 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 2 |
Data Collection
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 (All) | R-Work (Depositor) | R-Free (Depositor) | Mean Isotropic B | ||||||||
| ELECTRON CRYSTALLOGRAPHY | FREE R-VALUE | 1.09 | 56.82 | 98240 | 4971 | 97.237 | 0.151 | 0.1498 | 0.1831 | 11.288 | |||||||||
| 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] | |
| 0.618 | 0.618 | -1.236 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_6_deg | 17.18 |
| r_lrange_it | 16.209 |
| r_lrange_other | 15.162 |
| r_dihedral_angle_3_deg | 11.08 |
| r_dihedral_angle_2_deg | 8.674 |
| r_scangle_it | 6.361 |
| r_scangle_other | 6.36 |
| r_dihedral_angle_1_deg | 6.358 |
| r_rigid_bond_restr | 5.633 |
| r_scbond_other | 4.785 |
| Sample |
|---|
| Proteinase K |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 3D ARRAY |
| Vitrification Instrument | LEICA PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | CRYSTALLOGRAPHY |
| Number of Particles | |
| Reported Resolution (Å) | 1.09 |
| Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
| Other Details | |
| Refinement Type | |
| Symmetry Type | 3D CRYSTAL |
| Space Group Name | |
| Length a | 66.92 |
| Length b | 66.92 |
| Length c | 66.92 |
| Angle Alpha | 90 |
| Angle Beta | 90 |
| Angle Gamma | 90 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5kxv) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | Maximum likelihood | ||||
| Overall B Value | 11.29 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 0.002 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | DIFFRACTION |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | 4.2.0 |
| MODEL FITTING | Coot | 0.9.8.93 |
| MOLECULAR REPLACEMENT | PHASER | 2.8.3 |
| SYMMETRY DETERMINATION | XDS | BUILT=20230630 |
| CRYSTALLOGRAPHY MERGING | XSCALE | BUILT=20230630 |
| RECONSTRUCTION | phenix.refine | 1.21.1 |
| MODEL REFINEMENT | PHENIX | 1.21.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
