5KMG
Near-atomic cryo-EM structure of PRC1 bound to the microtubule
ELECTRON MICROSCOPY
| Sample |
|---|
| Ternary complex of PRC1 fragment (PRC1-SC), alpha-tubulin, and beta-tubulin. |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | HELICAL ARRAY |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | blot for 4 seconds, blot force 10 |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 17069 |
| Reported Resolution (Å) | 3.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 8.67 |
| Angular Rotation | -25.76 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3NRX, 4L6Y) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 8 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
| Nominal Magnification | 27500 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | Leginon | 3.2 |
| IMAGE ACQUISITION | Appion | 3.2 |
| CTF CORRECTION | CTFFIND | 4 |
| MODEL FITTING | UCSF Chimera | 1.10 |
| MODEL REFINEMENT | I-TASSER | 4.4 |
| MODEL REFINEMENT | iMODFIT | 1.04 |
| MODEL REFINEMENT | Rosetta | 3.6 |
| INITIAL EULER ASSIGNMENT | EMAN2 | 2.07 |
| FINAL EULER ASSIGNMENT | FREALIGN | 9.09 |
| RECONSTRUCTION | FREALIGN | 9.09 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 27275 | manually selected microtubule filaments using manualpicker.py | ||
