5VOS
VGSNKGAIIGL from Amyloid Beta determined by MicroED
ELECTRON CRYSTALLOGRAPHY
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | Batch | 4 | 310 | 50 mM sodium citrate, pH 4.0, 10% v/v DMSO |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.42 | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 18.78 | α = 90 |
| b = 4.73 | β = 100.02 |
| c = 33.47 | 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 F416 CMOS CAMERA | 2015-04-17 | |||||||||
| 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 | 1.42 | 32.96 | 85.5 | 0.222 | 0.244 | 0.98 | 4.88 | 5.175 | 1129 | -3 | 14.635 | ||||||||
| 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 | 1.42 | 1.49 | 47.5 | 0.496 | 0.611 | 0.452 | 1.09 | 2.571 | |||||||||||
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 | 1.42 | 32.96 | 1014 | 113 | 85.51 | 0.2389 | 0.2335 | 0.2924 | RANDOM | 13.166 | |||||||
| 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] | |
| 1.04 | 0.83 | -1.3 | -0.04 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 52.256 |
| r_dihedral_angle_3_deg | 15.734 |
| r_dihedral_angle_1_deg | 8.714 |
| r_angle_refined_deg | 1.838 |
| r_angle_other_deg | 0.659 |
| r_chiral_restr | 0.076 |
| r_bond_refined_d | 0.016 |
| r_gen_planes_refined | 0.005 |
| r_bond_other_d | 0.003 |
| r_gen_planes_other | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 72 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XSCALE | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| Sample |
|---|
| Fibrils of Amyloid Beta segment 24-34 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 3D ARRAY |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| 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 | 18.78 |
| Length b | 4.73 |
| Length c | 4.73 |
| Angle Alpha | 90 |
| Angle Beta | 100.017 |
| Angle Gamma | 90 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | Maximum likelihood | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TVIPS TEMCAM-F416 (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 0.03 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| 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 | TVIPS TemCam-F416 | |
| MODEL FITTING | Coot | |
| MOLECULAR REPLACEMENT | phaser | |
| CRYSTALLOGRAPHY MERGING | XSCALE | Jun 17, 2015 |
| MODEL REFINEMENT | Refmac5 | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
