6DPU

Undecorated GMPCPP microtubule


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.068
r_dihedral_angle_3_deg16.033
r_dihedral_angle_1_deg12.204
r_dihedral_angle_4_deg11.901
r_long_range_B_refined4.302
r_long_range_B_other4.302
r_mcangle_it1.771
r_mcangle_other1.771
r_angle_refined_deg1.445
r_scangle_other1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.068
r_dihedral_angle_3_deg16.033
r_dihedral_angle_1_deg12.204
r_dihedral_angle_4_deg11.901
r_long_range_B_refined4.302
r_long_range_B_other4.302
r_mcangle_it1.771
r_mcangle_other1.771
r_angle_refined_deg1.445
r_scangle_other1.36
r_angle_other_deg0.972
r_mcbond_it0.947
r_mcbond_other0.947
r_scbond_it0.695
r_scbond_other0.695
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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
microtubule stabilized by GMPCPP
Specimen Preparation
Sample Aggregation StateHELICAL ARRAY
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot for 4 seconds before plunging.
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles110127
Reported Resolution (Å)3.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise8.99
Angular Rotation-25.75
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCorrelation coefficient
Overall B Value150
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)1.33
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.01
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONAppion
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf
MODEL FITTINGUCSF Chimera
MODEL REFINEMENTREFMAC
INITIAL EULER ASSIGNMENTEMAN
FINAL EULER ASSIGNMENTFREALIGN
RECONSTRUCTIONFREALIGN
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION