6VRS

Single particle reconstruction of glucose isomerase from Streptomyces rubiginosus based on data acquired in the presence of substantial aberrations


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.248
r_dihedral_angle_4_deg16.595
r_long_range_B_refined16.001
r_dihedral_angle_3_deg13.633
r_mcangle_it8.608
r_scbond_it7.081
r_mcbond_it5.417
r_dihedral_angle_1_deg5.405
r_angle_refined_deg1.602
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.248
r_dihedral_angle_4_deg16.595
r_long_range_B_refined16.001
r_dihedral_angle_3_deg13.633
r_mcangle_it8.608
r_scbond_it7.081
r_mcbond_it5.417
r_dihedral_angle_1_deg5.405
r_angle_refined_deg1.602
r_chiral_restr0.115
r_gen_planes_refined0.008
r_bond_refined_d0.007
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
glucose isomerase
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles61909
Reported Resolution (Å)2.7
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsWe used the approach implemented in cisTEM.
Refinement Type
Symmetry TypePOINT
Point SymmetryD2
Map-Model Fitting and Refinement
Id1 (5VR0)
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 CORRECTION114522