9ZC6 | pdb_00009zc6

5-methyl-cytidine L-21 ScaI Tetrahymena Ribozyme

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7XSN

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.0271
f_angle_d	0.4036
f_chiral_restr	0.0216
f_plane_restr	0.0024
f_bond_d	0.0014

Sample
5mC-TR

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	233268
Reported Resolution (Å)	4.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (7XSN)
Refinement Space
Refinement Protocol	FLEXIBLE FIT
Refinement Target	geometry minimization
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	30

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS GLACIOS
Minimum Defocus (nm)	500
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
PARTICLE SELECTION	cryoSPARC
MODEL FITTING	UCSF ChimeraX
MODEL FITTING	Rosetta
RECONSTRUCTION	cryoSPARC	4.6.2
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

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