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Cryo-EM structure of the full-length Bacillus subtilis glyQS T-box riboswitch in complex with tRNA-Gly
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LCK
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.697 f_angle_d 0.808 f_chiral_restr 0.03 f_plane_restr 0.003 f_bond_d 0.002
Sample T-box-tRNAGly complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 uL sample
blot once for 3s
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 189361 Reported Resolution (Å) 4.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4LCK, 4LCK) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target model map cross correlation Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 38
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 400 Maximum Defocus (nm) 3500 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU 1.10 CTF CORRECTION CTFFIND 4.1.18 CTF CORRECTION RELION 3.0-beta MODEL FITTING UCSF Chimera 1.13.1 INITIAL EULER ASSIGNMENT RELION 3.0-beta FINAL EULER ASSIGNMENT RELION 3.0-beta CLASSIFICATION RELION 3.0-beta CLASSIFICATION cryoSPARC 2.2 RECONSTRUCTION RELION 3.0-beta RECONSTRUCTION cryoSPARC 2.2 MODEL REFINEMENT PHENIX 1.15.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 1962681 neural network particle picking module in EMAN2.2