8JLE

Cryo-EM structure of SV2A LD4 in complex with BoNT/A2 Hc in the SV2A-levetiracetam-BoNT/A2 Hc complex


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined39.759
r_long_range_B_other39.758
r_scangle_other25.969
r_mcangle_it21.087
r_mcangle_other21.084
r_scbond_it16.605
r_scbond_other16.602
r_mcbond_it14.343
r_mcbond_other14.341
r_dihedral_angle_3_deg13.714
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined39.759
r_long_range_B_other39.758
r_scangle_other25.969
r_mcangle_it21.087
r_mcangle_other21.084
r_scbond_it16.605
r_scbond_other16.602
r_mcbond_it14.343
r_mcbond_other14.341
r_dihedral_angle_3_deg13.714
r_dihedral_angle_1_deg5.714
r_dihedral_angle_2_deg4.223
r_angle_refined_deg1.414
r_angle_other_deg0.456
r_chiral_restr0.068
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.001
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
SV2A in complex with BoNT/A2 Hc domain and anti-epileptic drug, levetiracetam
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles646723
Reported Resolution (Å)2.82
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 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50.8
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC
CTF CORRECTIONcryoSPARC
MODEL FITTINGCoot
MODEL REFINEMENTREFMAC
INITIAL EULER ASSIGNMENTcryoSPARC
FINAL EULER ASSIGNMENTcryoSPARC
CLASSIFICATIONcryoSPARC
RECONSTRUCTIONcryoSPARC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION6409122