3J8F
Cryo-EM reconstruction of poliovirus-receptor complex
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 5.397 |
| r_dihedral_angle_3_deg | 2.307 |
| r_angle_refined_deg | 2.032 |
| r_dihedral_angle_4_deg | 1.866 |
| r_dihedral_angle_1_deg | 0.335 |
| r_chiral_restr | 0.154 |
| r_bond_refined_d | 0.01 |
| r_gen_planes_refined | 0.002 |
| Sample |
|---|
| Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155) |
| Sample Components |
| Human poliovirus 1 Mahoney |
| Poliovirus receptor |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Sample mixed and frozen within 2 minutes before plunging into liquid ethane. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 9248 |
| Reported Resolution (Å) | 4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | (Single particle--Applied symmetry: I) |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1HXS, 1HXS, 1HXS, 1HXS, 4FQP) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | pseudo-real space | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFINEMENT PROTOCOL--flexible DETAILS--After rigid-body fitting, manual rebuilding of the model was alternated with automated stereochemically restr ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 25 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2013-11-01 |
| Temperature (Kelvin) | 100 |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.26 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | OTHER |
| Nominal Magnification | 27500 |
| Calibrated Magnification | 25355 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | K2 Summit super-resolution mode used |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | Coot | |
| MODEL FITTING | REFMAC | 5 |
| MODEL FITTING | SPDBV | |
| RECONSTRUCTION | FREALIGN | |
| RECONSTRUCTION | RELION | 1.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| per micrograph | ||||
