7S6D
CryoEM structure of modular PKS holo-Lsd14 bound to antibody fragment 1B2, composite structure
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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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 |
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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 | |
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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 | |
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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 | |||||
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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 | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 54 |
Imaging Experiment | 1 |
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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 | ||
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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 | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 295592 |