9ZGO | pdb_00009zgo

Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 6

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9OV3

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	24.364
f_angle_d	0.497
f_chiral_restr	0.026
f_plane_restr	0.004
f_bond_d	0.002

Sample
ribonuclease P RNA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Grids were glow-discharged on both sides prior to vitrification. Vitrification was performed using a Vitrobot Mark IV with a 10s wait time, followed by a 3s blot and blot force 3 to 10

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	80440
Reported Resolution (Å)	3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (9OV3)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	maximization of map-to-model correlation
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	53

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
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)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.6
IMAGE ACQUISITION	EPU	3
CTF CORRECTION	cryoSPARC	4.6
RECONSTRUCTION	cryoSPARC	4.6
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