7RVF
Segment from the Y169F mutant of the bank vole prion protein 168-176 QFNNQNNFV
ELECTRON CRYSTALLOGRAPHY
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 0.2 M MES, pH 6, 10% MPD |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 4.88 | α = 93.89 |
b = 10.56 | β = 92.38 |
c = 29.98 | γ = 103.29 |
Symmetry | |
---|---|
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 | 2017-03-22 | 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 | 10.24 | 94.8 | 0.229 | 0.248 | 0.98 | 5.33 | 6.239 | 2938 | 8.937 |
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 | 54.9 | 0.636 | 0.7 | 0.711 | 2.28 | 5.154 |
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 | 10.24 | 2644 | 294 | 94.77 | 0.2202 | 0.2167 | 0.2506 | RANDOM | 6.086 |
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] | |
0.01 | 0.01 | -0.02 | -0.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 49.699 |
r_dihedral_angle_3_deg | 11.357 |
r_dihedral_angle_1_deg | 4.788 |
r_angle_refined_deg | 1.662 |
r_angle_other_deg | 1.318 |
r_chiral_restr | 0.062 |
r_gen_planes_refined | 0.009 |
r_bond_refined_d | 0.008 |
r_bond_other_d | 0.001 |
r_gen_planes_other |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 79 |
Nucleic Acid Atoms | |
Solvent Atoms | 2 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SHELXD | phasing |
Sample |
---|
Major prion protein |
Specimen Preparation | |
---|---|
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 | 4.88 |
Length b | 10.56 |
Length c | 10.56 |
Angle Alpha | 103.29 |
Angle Beta | 92.38 |
Angle Gamma | 103.29 |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | TVIPS TEMCAM-F416 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) |
Imaging Experiment | 1 |
---|---|
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 |