8PN1 | pdb_00008pn1

CryoEM structure of Nal1 protein, allele SPIKE, from Oryza sativa japonica group

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8PME

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.1244
f_angle_d	0.5792
f_chiral_restr	0.0454
f_plane_restr	0.0042
f_bond_d	0.0024

Sample
Nal1

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	72613
Reported Resolution (Å)	2.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	D3

Map-Model Fitting and Refinement
Id	1 (8PME)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	49.02

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	5000
Maximum Defocus (nm)	50000
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
PARTICLE SELECTION	RELION	4.0
IMAGE ACQUISITION	SerialEM	3.8.4
CTF CORRECTION	RELION	4.0
MODEL FITTING	PHENIX	1.21rc1_4903
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	PHENIX	1.21rc1_4903

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		216590