3JBD
Complex of poliovirus with VHH PVSP6A
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 19.07 |
| r_dihedral_angle_3_deg | 8.162 |
| r_dihedral_angle_4_deg | 6.475 |
| r_angle_refined_deg | 1.771 |
| r_dihedral_angle_1_deg | 1.522 |
| r_chiral_restr | 0.122 |
| r_bond_refined_d | 0.008 |
| r_gen_planes_refined | 0.003 |
| Sample |
|---|
| Nanobody AB6 in complex with poliovirus P1/Mahoney |
| Sample Components |
| Human poliovirus 1 |
| Nanobody PVPS6A |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blotted for 2 seconds before plunging into liquid ethane (homemade plunger). |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 57282 |
| Reported Resolution (Å) | 4.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | (Single particle details: The particles were processed using frealign.) (Single particle--Applied symmetry: I) |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1HXS, 2PLV, 4BEL, 2X1P) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Stereochemically restrained maximum likelihood refinement of both Fourier phase and amplitude agreement | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFINEMENT PROTOCOL--Rigid body with some flexible loops and side chains DETAILS--LSQKAB was applied after each refinement cycle to re-impose exact ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN ULTRASCAN 4000 (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 25 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2012-10-17 |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.6 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 96000 |
| Calibrated Magnification | 89232 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | Coot | |
| MODEL FITTING | REFMAC | 5 |
| MODEL FITTING | SPDBV | |
| RECONSTRUCTION | FREALIGN | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| per particle | ||||
