7S6D
CryoEM structure of modular PKS holo-Lsd14 bound to antibody fragment 1B2, composite structure
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.3301 |
| f_angle_d | 0.6399 |
| f_chiral_restr | 0.0425 |
| f_plane_restr | 0.0047 |
| f_bond_d | 0.0032 |
| Sample |
|---|
| Dimeric holo-Lsd14 containing docking domains from DEBS module 3 (holo-Lsd14-DD*) bound to two copies each of Fab 1B2 light and heavy chains and NADP. |
| Sample Components |
| Polyketide synthase |
| Fab 1B2 heavy chain, Fab 1B2 light chain |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot for 5 seconds before plunging in liquid ethane. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 295592 |
| Reported Resolution (Å) | 3.1 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Composite map was generated by combining the unsharpened focused maps for KSAT dimer (EMD-24870), LDAT domains (EMD-24871), LD'AT' domains (EMD-24872) ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7S6B, 6C9U, 6C9U) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Model was rebuilt in coot and refined using phenix.real_space_refine. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 54 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2700 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 63000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.2.0 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | cryoSPARC | 3.2.0 |
| CTF CORRECTION | RELION | 3.1 |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | PHENIX | |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
| FINAL EULER ASSIGNMENT | RELION | 3.1 |
| RECONSTRUCTION | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 295592 | |||
