7V0K | pdb_00007v0k

Consensus refinement of human erythrocyte ankyrin-1 complex (Composite map)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YZF

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.74
f_angle_d	0.64
f_chiral_restr	0.043
f_plane_restr	0.006
f_bond_d	0.003

Sample
Band 3 anion exchanger complexed with glycophorin A, in outward facing state

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	4-6 seconds, wait time 30 seconds

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	710734
Reported Resolution (Å)	2.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Main map corresponds to a composite map of EMD-26916 (RhAG/CE+ankyrin-1 (AR1-5), EMD-26917 (Protein 4.2), EMD-26918 (Ankyrin-1), EMD-26919 (Band3-I cy ...	Main map corresponds to a composite map of EMD-26916 (RhAG/CE+ankyrin-1 (AR1-5), EMD-26917 (Protein 4.2), EMD-26918 (Ankyrin-1), EMD-26919 (Band3-I cytoplasmic domains), EMD-26940 (Band3-I TM domains). The consensus global refinement is provided in additional maps.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4YZF)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	58

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	1500
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
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	Leginon
CTF CORRECTION	cryoSPARC	3
MODEL FITTING	Coot	0.9.8
MODEL REFINEMENT	PHENIX	1.20.1
INITIAL EULER ASSIGNMENT	cryoSPARC	3
FINAL EULER ASSIGNMENT	cryoSPARC	3
RECONSTRUCTION	cryoSPARC	3

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Patch CTF (cryoSPARC v3) followed by per particle defocus refinement and refinement of higher order aberrations (cryoSPARC v3)