6EO1 | pdb_00006eo1

The electron crystallography structure of the cAMP-bound potassium channel MloK1 (PCO-refined)

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

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

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 252.45	α = 90
b = 252.45	β = 90
c = 209	γ = 90

Symmetry
Space Group	P 4 21 2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY		NONE	4.5	6	23102		100

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.049
f_angle_d	0.934
f_chiral_restr	0.047
f_bond_d	0.013
f_plane_restr	0.007

Software

Software
Software Name	Purpose
PHENIX	refinement

Sample
MloK1 tetramer

Specimen Preparation
Sample Aggregation State	2D ARRAY
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	3.5 second-blotting

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	4.5
Resolution Method	OTHER
Other Details
Refinement Type
Symmetry Type	2D CRYSTAL
Space Group Name	P 4 21 2
Length a	135
Length b	135
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1 (4CHV)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	fit energy
Overall B Value
Fitting Procedure
Details	The initial model was obtained using Modeller (Sali and Blundell, 1993); in particular, the missing fragments were generated for the previously publis ...	The initial model was obtained using Modeller (Sali and Blundell, 1993); in particular, the missing fragments were generated for the previously published PDB 4CHV model. This starting model was refined using the Rosetta for cryo-EM package (DiMaio et al., 2015). The symmetry of the channel was restrained during optimization runs (performed following the package tutorial (Wang and DiMaio,2015)). A model with a high fit score to the cryo-EM map and a low energy, as defined by the Rosetta force field, was selected from 100 Rosetta models generated and refined further. Several rounds of manual refinement with Coot (Emsley et al.,2010) and global optimization with Phenix (real_space_refine method (Afonine et al., 2013)) were carried out. Secondary structure constraints were imposed to stabilize the fold of helices and b-sheets during the global optimization.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	45

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	750
Maximum Defocus (nm)	4300
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	50000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	pixel size 1.3 A/pix

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	FOCUS	1.0
MODEL FITTING	Rosetta
MODEL REFINEMENT	PHENIX

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

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.