7RVK
Segment from Y169G mutant of the human prion protein 169-175 GSNQNNF
ELECTRON CRYSTALLOGRAPHY
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 10% w/v PEG8000, 0.1 M MES, pH 6, 0.2 M sodium acetate |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 4.86 | α = 90 |
b = 14.11 | β = 93.71 |
c = 18.41 | γ = 101.21 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | electron | 100 | CMOS | TVIPS TEMCAM-F416 | 2016-09-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ELECTRON MICROSCOPE | OTHER | 0.0251 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 13.84 | 80.3 | 0.238 | 0.257 | 0.98 | 5.05 | 6.217 | 2076 | 3.58 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1 | 1.03 | 64.7 | 0.43 | 0.485 | 0.862 | 2.25 | 4.26 |
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 | AB INITIO PHASING | THROUGHOUT | 1 | 13.84 | 2075 | 208 | 80.3 | 0.2024 | 0.1984 | 0.2382 | RANDOM | 5.74 |
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] | |
-0.0165 | 0.1179 | 0.2173 | 0.2353 | -0.1016 | -0.2188 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 24.6 |
t_omega_torsion | 3.14 |
t_angle_deg | 0.94 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 55 |
Nucleic Acid Atoms | |
Solvent Atoms | 6 |
Heterogen Atoms | 8 |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data scaling |
BUSTER | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SHELXD | phasing |
Sample |
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Major prion protein |
Specimen Preparation | |
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Sample Aggregation State | 3D ARRAY |
3D Reconstruction | |
---|---|
Reconstruction Method | CRYSTALLOGRAPHY |
Number of Particles | |
Reported Resolution (Å) | 1 |
Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
Other Details | |
Refinement Type | |
Symmetry Type | 3D CRYSTAL |
Space Group Name | |
Length a | 4.86 |
Length b | 14.11 |
Length c | 14.11 |
Angle Alpha | 101.21 |
Angle Beta | 93.71 |
Angle Gamma | 101.21 |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | TVIPS TEMCAM-F416 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TECNAI F30 |
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) | 300 |
Imaging Details |