6VSA

Single particle reconstruction of HemQ from Geobacillus based on data acquired in the presence of substantial aberrations


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T0T 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.772
r_long_range_B_refined31.106
r_dihedral_angle_3_deg19.637
r_mcangle_it18.53
r_scbond_it17.99
r_dihedral_angle_4_deg16.596
r_mcbond_it14.196
r_dihedral_angle_1_deg6.794
r_angle_refined_deg2.074
r_chiral_restr0.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.772
r_long_range_B_refined31.106
r_dihedral_angle_3_deg19.637
r_mcangle_it18.53
r_scbond_it17.99
r_dihedral_angle_4_deg16.596
r_mcbond_it14.196
r_dihedral_angle_1_deg6.794
r_angle_refined_deg2.074
r_chiral_restr0.138
r_bond_refined_d0.012
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
HemQ
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles81302
Reported Resolution (Å)2.32
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC5
Map-Model Fitting and Refinement
Id1 (1T0T)
Refinement SpaceRECIPROCAL
Refinement ProtocolOTHER
Refinement TargetREFMAC
Overall B Value
Fitting Procedure
DetailsCOOT was crucial as well.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)120
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS TALOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
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)200
Imaging DetailsThe goal of the experiment was to show that it is possible to perform high resolution reconstruction in the presence of higher order aberrations.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcisTEM
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcisTEM
MODEL FITTINGMOLREP
INITIAL EULER ASSIGNMENTcisTEM
MODEL REFINEMENTREFMAC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION156210