9L8O | pdb_00009l8o

Structure of SID-1 in complex with dsRNA (dodecameric form)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOther 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_other44.072
r_lrange_it44.071
r_dihedral_angle_2_deg32.648
r_mcangle_it24.181
r_mcangle_other24.177
r_scangle_it22.129
r_scangle_other22.127
r_dihedral_angle_4_deg18.465
r_dihedral_angle_3_deg14.893
r_mcbond_other14.512
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_other44.072
r_lrange_it44.071
r_dihedral_angle_2_deg32.648
r_mcangle_it24.181
r_mcangle_other24.177
r_scangle_it22.129
r_scangle_other22.127
r_dihedral_angle_4_deg18.465
r_dihedral_angle_3_deg14.893
r_mcbond_other14.512
r_mcbond_it14.509
r_scbond_other12.664
r_scbond_it12.663
r_paralell_plane_angle_deg12.321
r_dihedral_angle_1_deg7.683
r_angle_refined_deg1.702
r_angle_other_deg1.332
r_nbd_other0.528
r_symmetry_xyhbond_nbd_refined0.273
r_symmetry_nbd_refined0.194
r_nbd_refined0.18
r_nbtor_refined0.151
r_xyhbond_nbd_refined0.134
r_symmetry_nbd_other0.122
r_chiral_restr0.091
r_symmetry_nbtor_other0.066
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_gen_planes_other0.004
r_bond_other_d
Sample
SID-1 in complex with dsRNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles52278
Reported Resolution (Å)3.99
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD6
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)48
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC
IMAGE ACQUISITIONSerialEM
MODEL FITTINGCoot0.9.6
MODEL REFINEMENTServalcat0.4.88
RECONSTRUCTIONcryoSPARC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1772453