8UBA | pdb_00008uba

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Pre-active state 1b


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined46.328
r_long_range_B_other46.327
r_scangle_other30.611
r_mcangle_it26.135
r_mcangle_other26.133
r_dihedral_angle_3_deg20.524
r_scbond_it19.574
r_scbond_other19.572
r_mcbond_it17.532
r_mcbond_other17.53
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined46.328
r_long_range_B_other46.327
r_scangle_other30.611
r_mcangle_it26.135
r_mcangle_other26.133
r_dihedral_angle_3_deg20.524
r_scbond_it19.574
r_scbond_other19.572
r_mcbond_it17.532
r_mcbond_other17.53
r_dihedral_angle_1_deg6.133
r_dihedral_angle_2_deg4.953
r_angle_refined_deg1.55
r_angle_other_deg0.46
r_chiral_restr0.108
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Diversity-generating retroelement (DGR) ribonucleoprotein with dCpCpp
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles121652
Reported Resolution (Å)3.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)55
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)400
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION
PARTICLE SELECTIONcryoSPARC
PARTICLE SELECTIONTopaz
PARTICLE SELECTIONGautomatch
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONGctf
CTF CORRECTIONCTFFIND
MODEL FITTINGCoot
CLASSIFICATIONcryoSPARC
RECONSTRUCTIONcryoSPARC3.1.1
MODEL REFINEMENTCCP4 package
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY