5V5B
KVQIINKKLD, Structure of the amyloid spine from microtubule associated protein tau Repeat 2
ELECTRON CRYSTALLOGRAPHY
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.2 | 310 | 0.1 M phosphate citrate, 32% PEG10000 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.74 | 29.23 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 27.12 | α = 90 |
b = 4.83 | β = 100.53 |
c = 32.43 | γ = 90 |
Symmetry | |
---|---|
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 TEMCAM-F416 | 2016-08-25 |
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) | 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 | 1.5 | 18.83 | 84.8 | 0.255 | 0.268 | 0.984 | 5.24 | 9.133 | 2203 | -3 | 8.37 |
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 | 1.5 | 1.56 | 85.9 | 0.419 | 0.452 | 0.849 | 2.83 | 6.214 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.5 | 18.83 | 1313 | 132 | 82.37 | 0.1927 | 0.1904 | 0.2127 | RANDOM | 16.92 |
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] | |
-5.1394 | 3.5054 | 4.6904 | 0.4491 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 11.91 |
t_omega_torsion | 4.31 |
t_angle_deg | 1.51 |
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 | 81 |
Nucleic Acid Atoms | |
Solvent Atoms | 2 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
BUSTER | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Sample |
---|
KVQIINKKLD Tau peptide |
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) | |
Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
Other Details | |
Refinement Type | |
Symmetry Type | 3D CRYSTAL |
Space Group Name | |
Length a | 27.12 |
Length b | 4.83 |
Length c | 4.83 |
Angle Alpha | 90 |
Angle Beta | 105.53 |
Angle Gamma | 90 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | |||||
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) | 0.1 |
Imaging Experiment | 1 |
---|---|
Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TECNAI 20 |
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 | Coot | 0.84 |
MODEL REFINEMENT | BUSTER | 2.10.0 |
Image Processing | ||||
---|---|---|---|---|
CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
NONE |