7PTP | pdb_00007ptp

In-situ structure of pentameric S-layer protein

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.725
f_angle_d	0.608
f_chiral_restr	0.046
f_bond_d	0.003
f_plane_restr	0.003

Sample
In-situ structure of pentameric S-layer of Haloferax volcanii

Specimen Preparation
Sample Aggregation State	CELL
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Vitrobot options: Blot time 2.0 seconds, Blot force -15,1, Wait time 0 seconds, Drain time 0.5 seconds

3D Reconstruction
Reconstruction Method	SUBTOMOGRAM AVERAGING
Number of Particles	1640
Reported Resolution (Å)	11.58
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C5

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Best Fit
Overall B Value
Fitting Procedure
Details	Rigid body fit inside coot of D1-D6 domains and real space refinement with restraints of the original model obtained by single particle analysis in PHENIX.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	2.9

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	4000
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	105000
Calibrated Magnification	105000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	SerialEM Hagen Scheme

EM Software
Task	Software Package	Version
VOLUME SELECTION	RELION	3.1
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	CTFFIND	4.1.13
MODEL FITTING	Coot	0.9.2-pre
INITIAL EULER ASSIGNMENT	RELION	3.0
FINAL EULER ASSIGNMENT	RELION	3.1
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.19-4092

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	RELION subtomogram averaging (Bharat & Scheres 2016)	1773652	Particles were initially picking using the Laplacian-of gaussian algorithm implemented in RELION3.0 (Zivanov et al., 2018). Particles were extracted in 8x down-sampled in 50x50 pixel boxes and classified using reference-free 2D classification inside RELION3.0.