6ZET
Crystal structure of proteinase K nanocrystals by electron diffraction with a 20 micrometre C2 condenser aperture
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ID8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.365 | α = 90 |
b = 67.365 | β = 90 |
c = 106.784 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Data Collection
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
2.7 | 2.83 | 83.6 | 1.275 | 1.389 | 0.533 | 0.498 | 1.8 | 10.5 |
Refinement
Statistics | |||||||||||||||||||
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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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
ELECTRON CRYSTALLOGRAPHY | MOLECULAR REPLACEMENT | FREE R-VALUE | 2ID8 | 2.701 | 57.04 | 6184 | 297 | 85.925 | 0.227 | 0.2247 | 0.2679 | 7.281 |
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] | |
-0.134 | -0.134 | 0.267 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.442 |
r_dihedral_angle_4_deg | 19.975 |
r_dihedral_angle_3_deg | 16.12 |
r_scangle_it | 5.536 |
r_lrange_it | 5.499 |
r_dihedral_angle_1_deg | 5.026 |
r_scbond_it | 4.897 |
r_mcangle_it | 3.796 |
r_mcbond_it | 2.992 |
r_angle_refined_deg | 1.207 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Sample |
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proteinase K |
Specimen Preparation | |
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Sample Aggregation State | 3D ARRAY |
Vitrification Instrument | |
Cryogen Name | ETHANE |
Sample Vitrification Details | Excess liquid was removed by blotting for 4-6s with a Vitrobot |
3D Reconstruction | |
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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 | 67.3653 |
Length b | 67.3653 |
Length c | 67.3653 |
Angle Alpha | 90 |
Angle Beta | 90 |
Angle Gamma | 90 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (2ID8) | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | |||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | OTHER | OTHER | OTHER | OTHER | OTHER | OTHER | OTHER | OTHER | |
Electron Dose (electrons/Å**2) | 0.034 | 0.034 | 0.034 | 0.034 | 0.034 | 0.034 | 0.034 | 0.034 |
Imaging Experiment | 1 |
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Date of Experiment | 2018-04-20 |
Temperature (Kelvin) | |
Microscope Model | FEI TALOS ARCTICA |
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 |
EM Software | ||
---|---|---|
Task | Software Package | Version |
MOLECULAR REPLACEMENT | Phaser | 2.8.2 |
SYMMETRY DETERMINATION | POINTLESS | 1.11.12 |
CRYSTALLOGRAPHY MERGING | AIMLESS | 0.7.1 |
MODEL REFINEMENT | REFMAC | 5.8.0258 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |