9NN1 | pdb_00009nn1

Yeast V1-ATPase bound to Rtc5p

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7TMM
experimental model	PDB	9MOY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.4212
f_angle_d	0.4688
f_chiral_restr	0.0394
f_plane_restr	0.0033
f_bond_d	0.0026

Sample
Yeast V1-ATPase bound to Rtc5p

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	67351
Reported Resolution (Å)	3.7
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (7tmm, 9moy)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)	49.25

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS GLACIOS
Minimum Defocus (nm)	400
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	ISOLDE
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	RELION	5
FINAL EULER ASSIGNMENT	RELION	5
CLASSIFICATION	RELION	5
RECONSTRUCTION	RELION	5
MODEL REFINEMENT	PHENIX	1.21_5207

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		556655