7PTL | pdb_00007ptl

Mature conformer of a 6-helix bundle of RNA with clasp

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D1B

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.002
f_angle_d	1.003
f_chiral_restr	0.06
f_plane_restr	0.007
f_bond_d	0.005

Sample
Mature conformer of a 6-helix bundle of RNA with clasp

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	3 microlitre droplet, 4 second delay before blotting, 6 second blot, 0 second delay before plunging.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	337099
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 (2D1B)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Correlation Coefficient
Overall B Value	303
Fitting Procedure
Details	Helical templates and tetraloops were generated in RNAbuild. Kissing loops were modelling based on the PDB:2D1B structure. A combination of PHENIX RSR and ISOLDE were used to arrive at the final structure.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	750
Maximum Defocus (nm)	2500
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	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	3.2.0
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC	3.2.0
MODEL FITTING	UCSF ChimeraX	1.2
MODEL FITTING	ISOLDE	1.2
MODEL REFINEMENT	PHENIX	1.19.2-4158-000
INITIAL EULER ASSIGNMENT	cryoSPARC	3.2.0
FINAL EULER ASSIGNMENT	cryoSPARC	3.2.0
CLASSIFICATION	cryoSPARC	3.2.0
RECONSTRUCTION	cryoSPARC	3.2.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Patch CTF estimation (multi) from cryoSPARC.	1476537	Particle picking was performed using the template picker from cryoSPARC with templates generated from an ab initio model from the same dataset.