6U5G
MicroED structure of a FIB-milled CypA Crystal
ELECTRON CRYSTALLOGRAPHY
Crystallization
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.75 | 55.34 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 42.4 | α = 90 |
b = 53.4 | β = 90 |
c = 87.76 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Data Collection
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | Mean Isotropic B | ||||||
ELECTRON CRYSTALLOGRAPHY | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB entry 4YUM | 2.5 | 26.48 | 1.34 | 11440 | 396 | 86.01 | 0.1867 | 0.1854 | 0.2237 | 30.6 |
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 |
f_dihedral_angle_d | 12.8187 |
f_angle_d | 0.7321 |
f_chiral_restr | 0.0545 |
f_bond_d | 0.0112 |
f_plane_restr | 0.0053 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PHASER | phasing |
XDS | data scaling |
XDS | data reduction |
Sample |
---|
Peptidyl-prolyl cis-trans isomerase A |
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) | 2.5 |
Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
Other Details | |
Refinement Type | |
Symmetry Type | 3D CRYSTAL |
Space Group Name | |
Length a | 42.4 |
Length b | 53.4 |
Length c | 53.4 |
Angle Alpha | 90 |
Angle Beta | 90 |
Angle Gamma | 90 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (4YUM) | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | |||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | TVIPS TEMCAM-F416 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 0.06 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
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 |
MODEL FITTING | PHENIX | dev2880 |
MOLECULAR REPLACEMENT | PHENIX | dev2880 |
RECONSTRUCTION | PHENIX | dev2880 |
MODEL REFINEMENT | PHENIX | 1.16-3549 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
NONE |