9SKT | pdb_00009skt

Cryo-EM structure of H. neapolitanus CsoSCA in oxidizing conditions, dimer, minor state

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-O85042-F1

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	14.7745
s_dihedral_angle_3_deg	13.9166
s_dihedral_angle_1_deg	7.5508
s_dihedral_angle_2_deg	5.9887
s_angle_nonh_deg	2.1457
s_nbtor	0.2413
s_nbd	0.237
s_hbond_nbd	0.1932
s_chiral_restr	0.0915
s_bond_nonh_d	0.0131
s_planes	0.0088

Sample
HnCsoSCA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	4C, 100% relative humidity, delay time 0s, blot time 3s, blot force 0

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	277721
Reported Resolution (Å)	2.45
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The final reconstruction was produced by classifying dimers, regrouping similar 3D classes, and running local refinement with signal-subtracted particle images.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	RECIPROCAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	64.757

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	1800
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	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Topaz	0.2.5
IMAGE ACQUISITION	EPU	3.6.0
CTF CORRECTION	cryoSPARC	4.7
MODEL FITTING	UCSF ChimeraX	1.9
MODEL FITTING	ISOLDE	1.9
MODEL REFINEMENT	Servalcat	0.4.99
INITIAL EULER ASSIGNMENT	cryoSPARC	4.7
FINAL EULER ASSIGNMENT	cryoSPARC	4.7
CLASSIFICATION	cryoSPARC	4.7
RECONSTRUCTION	cryoSPARC	4.7

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		917605	Particles were picked with topaz, trained with a set of about 1000 particles picked manually from micrographs denoised by CryoSPARC. Topaz was trained and applied on raw micrographs. This is the number of hexamer particles.