9E0H | pdb_00009e0h

De novo calcium channel heptamer, CalC6_3 with DHR extensions. Off target multimerization state

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	2.888
f_angle_d	0.355
f_chiral_restr	0.028
f_plane_restr	0.002
f_bond_d	0.001

Sample
CalC6_3 with DHR extensions, hepatmer

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	45077
Reported Resolution (Å)	4.62
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C7

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	For the heptamer, CalC6_3 with DHR extension hexamer design model was used as a starting model. A single chain for the heptamer was isolated in PyMOL, ...	For the heptamer, CalC6_3 with DHR extension hexamer design model was used as a starting model. A single chain for the heptamer was isolated in PyMOL, and 7 copies of this chain were fitted to the map in UCSF Chimera to reform the channel. The heptamer was refined using several rounds of relaxation and minimization, performed on the complete structures, which were manually inspected for errors each time using ISOLDE in UCSF ChimeraX, Coot, and PHENIX real-space refinement. The final model quality was analyzed using MolProbity.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	47.32

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC
MODEL FITTING	UCSF Chimera
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	UCSF ChimeraX
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	PyMOL

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		886110

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.