5K2F
Structure of NNQQNY from yeast prion Sup35 with cadmium acetate determined by MicroED
ELECTRON CRYSTALLOGRAPHY
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 273 | 1.0 M sodium acetate, 0.1 M HEPES, pH 7.0, 0.01 M cadmium sulfate |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 22.074 | α = 90 |
b = 4.932 | β = 104.29 |
c = 23.51 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | 100 | CMOS | TVIPS F416 CMOS CAMERA | 2016-02-03 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ELECTRON MICROSCOPE | TECNAI F20 TEM | 0.0251 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 1 | 90 | 84.5 | 0.18 | 5.1 | 4.6 | 2564 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1 | 1.08 | 66 | 0.282 | 3.3 | 365 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
ELECTRON CRYSTALLOGRAPHY | THROUGHOUT | 1 | 22.79 | 2308 | 253 | 80.97 | 0.2223 | 0.2203 | 0.2415 | RANDOM | 6.444 |
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] | |
0.23 | 0.36 | -0.29 | -0.11 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 60.278 |
r_dihedral_angle_3_deg | 8.34 |
r_sphericity_free | 6.512 |
r_dihedral_angle_1_deg | 5.527 |
r_sphericity_bonded | 4.945 |
r_angle_refined_deg | 1.688 |
r_angle_other_deg | 0.957 |
r_rigid_bond_restr | 0.84 |
r_mcbond_it | 0.502 |
r_mcangle_it | 0.233 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 55 |
Nucleic Acid Atoms | |
Solvent Atoms | 7 |
Heterogen Atoms | 8 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data collection |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Sample |
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Prion fibril composed of a 6-residue segment of Sup35 and cadmium |
Specimen Preparation | |
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Sample Aggregation State | 3D ARRAY |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | Plunged into liquid ethane (FEI VITROBOT MARK IV) |
3D Reconstruction | |
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Reconstruction Method | CRYSTALLOGRAPHY |
Number of Particles | |
Reported Resolution (Å) | |
Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
Other Details | The density map was obtained using measured diffraction intensities and phases acquired from crystallographic direct methods program SHELXD. |
Refinement Type | |
Symmetry Type | 3D CRYSTAL |
Space Group Name | |
Length a | 22.074 |
Length b | 4.932 |
Length c | 4.932 |
Angle Alpha | 90 |
Angle Beta | 104.29 |
Angle Gamma | 90 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | OTHER | ||||
Refinement Target | maximum likelihood | ||||
Overall B Value | 6.44 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | TVIPS TEMCAM-F416 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 0.01 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TECNAI F20 |
Minimum Defocus (nm) | |
Maximum Defocus (nm) | |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | DIFFRACTION |
Specimen Holder Model | GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
IMAGE ACQUISITION | EM-Menu | 1 |
DIFFRACTION INDEXING | Denzo | 1.98.7 |
MODEL FITTING | Coot | 0.8.2 |
OTHER | SHELXD | 2013/2 |
MODEL REFINEMENT | refmac5 | 5.8.0135 |
CRYSTALLOGRAPHY MERGING | SCALEPACK | 1.98.7 |
RECONSTRUCTION | SHELXD | 2013/2 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
NONE |