6POM

Cryo-EM structure of the full-length Bacillus subtilis glyQS T-box riboswitch in complex with tRNA-Gly


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LCK 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.697
f_angle_d0.808
f_chiral_restr0.03
f_plane_restr0.003
f_bond_d0.002
Sample
T-box-tRNAGly complex
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details3 uL sample blot once for 3s
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles189361
Reported Resolution (Å)4.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (4LCK, 4LCK)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Targetmodel map cross correlation
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)38
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)400
Maximum Defocus (nm)3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification165000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEPU1.10
CTF CORRECTIONCTFFIND4.1.18
CTF CORRECTIONRELION3.0-beta
MODEL FITTINGUCSF Chimera1.13.1
INITIAL EULER ASSIGNMENTRELION3.0-beta
FINAL EULER ASSIGNMENTRELION3.0-beta
CLASSIFICATIONRELION3.0-beta
CLASSIFICATIONcryoSPARC2.2
RECONSTRUCTIONRELION3.0-beta
RECONSTRUCTIONcryoSPARC2.2
MODEL REFINEMENTPHENIX1.15.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY1962681neural network particle picking module in EMAN2.2