9UAJ | pdb_00009uaj

Ovorubin from the golden apple snail (Pomacea canaliculata)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	Other	AF-J7I2T6-F1
other	Other	AF-J7HZ90-F1
other	Other	AF-A0A2T7NVP5-F1
other	Other	AF-A0A2T7NVP6-F1

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.085
f_angle_d	0.609
f_chiral_restr	0.048
f_bond_d	0.006
f_plane_restr	0.004

Sample
Ovorubin

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	336633
Reported Resolution (Å)	2.12
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value	51.4
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	400
Maximum Defocus (nm)	1400
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	215000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.2.1
IMAGE ACQUISITION	EPU	3.3
CTF CORRECTION	cryoSPARC	4.6.0
MODEL FITTING	Coot	0.9.8.93
INITIAL EULER ASSIGNMENT	cryoSPARC	4.6.0
FINAL EULER ASSIGNMENT	cryoSPARC	4.6.0
CLASSIFICATION	cryoSPARC	4.2.1
RECONSTRUCTION	cryoSPARC	4.6.0
MODEL REFINEMENT	PHENIX	1.21.2_5419

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1621962