9QFP | pdb_00009qfp

Monomeric Photosystem I Cryo-EM structure at 1.8 A resolution

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	P0A405
in silico model	AlphaFold	P0A407
in silico model	AlphaFold	P0A415
in silico model	AlphaFold	P0A420
in silico model	AlphaFold	P0A423
in silico model	AlphaFold	P0A401
in silico model	AlphaFold	P0A427
in silico model	AlphaFold	P0A429
in silico model	AlphaFold	P0A425
in silico model	AlphaFold	P0A403
in silico model	AlphaFold	Q8DKP6

Sample
Monomeric photosystem I

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Delay time 30 s Blot time 2 s Blot force 0 Drain time 0 s

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	712866
Reported Resolution (Å)	1.74
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Resolution as reported by CryoSPARC, using its mask auto-tightening procedure.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Alphafold2 predictions fetched from AlphaFold-DB were placed into the map by rigid body fitting. Termini not supported by the map were trimmed. Every residue was visually inspected at least once, and its fit to density adjusted if necessary, using ISOLDE.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	400
Maximum Defocus (nm)	1400
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
CTF CORRECTION	cryoSPARC	4.5
MODEL FITTING	UCSF ChimeraX	1.8
INITIAL EULER ASSIGNMENT	cryoSPARC	4.5
FINAL EULER ASSIGNMENT	cryoSPARC	4.5
CLASSIFICATION	cryoSPARC	4.5
RECONSTRUCTION	cryoSPARC	4.5
MODEL REFINEMENT	ISOLDE	1.8
MODEL REFINEMENT	Servalcat	0.4.88

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Patch CTF estimation job in CryoSPARC, run with default settings.	1000224	Topaz was trained with a manually picked set of 1010 particles.