7S6C | pdb_00007s6c

CryoEM structure of modular PKS holo-Lsd14 stalled at the condensation step and bound to antibody fragment 1B2, composite structure

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7S6B
experimental model	PDB	6C9U

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.8619
f_angle_d	0.666
f_chiral_restr	0.0429
f_plane_restr	0.0047
f_bond_d	0.0033

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, treated with 2-Acetaminoethyl-thio-3-oxobutanoate
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	397539
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 KS-KS'-ACP domains (EMD-24863), LDAT domains (EMD-24864), LD'AT' domains (EMD-24865), KR domain (EMD-24866), Fab + DD* (EMD-24867), and the unsharpened consensus map (EMD-24862) using Combine Focused Maps in Phenix.
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 manually rebuilt in Coot and phenix.real_space_refine was used for refinement.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	53

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	79000
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
INITIAL EULER ASSIGNMENT	cryoSPARC	3.2.0
FINAL EULER ASSIGNMENT	RELION	3.1
RECONSTRUCTION	RELION	3.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		397539