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1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme - extended conformation
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 23.5078 f_angle_d 0.3999 f_chiral_restr 0.0218 f_plane_restr 0.0024 f_bond_d 0.0013
Sample L21-ScaI Tetrahymena ribozyme transcribed with 1-methyl-pseudouridine
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 60417 Reported Resolution (Å) 7.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7XSN) Refinement Space REAL 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) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC MODEL FITTING UCSF ChimeraX MODEL FITTING Rosetta MODEL REFINEMENT ISOLDE MODEL REFINEMENT PHENIX MODEL REFINEMENT Coot INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF 599317 Blob picking on denoised micrographs