9IHO | pdb_00009iho

Open state without NUQM and without flavoprotein (classification state 4) of Pichia pastoris mitochondrial complex I in cMSP26 nanodiscs

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	XXXX

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.0766
f_angle_d	0.4991
f_chiral_restr	0.0411
f_bond_d	0.0044
f_plane_restr	0.0039

Sample
Pichia Pastoris (Komagataella phaffi) mitochondrial complex I (NADH:ubiquinone oxidoreductase)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK III
Cryogen Name	ETHANE
Sample Vitrification Details	2s blot time and -10 blot force

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	18608
Reported Resolution (Å)	3.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (9ihr)
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details	The initial model was built into a map using ModelAngelo in RELION v5.0 to generate state 1. This model then had the required subunits deleted, and this was manually inspected in Coot and final refinements with ligand restraints imposed performed in PHENIX v.1.21_5207

Data Acquisition
Detector Type	TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)	47.79

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	RELION	4.0
PARTICLE SELECTION	Topaz
IMAGE ACQUISITION	EPU	3.6.0.6389
CTF CORRECTION	RELION	4.0
MODEL FITTING	Coot	0.9.8.92
INITIAL EULER ASSIGNMENT	cryoSPARC	3.3
FINAL EULER ASSIGNMENT	RELION	4.0
CLASSIFICATION	RELION	4.0
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	PHENIX	1.21_5207

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING ONLY		1350752