6DPV

Undecorated GDP microtubule


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.573
r_dihedral_angle_3_deg15.896
r_dihedral_angle_4_deg13.058
r_dihedral_angle_1_deg11.004
r_long_range_B_refined4.911
r_long_range_B_other4.911
r_mcangle_it2.059
r_mcangle_other2.059
r_scangle_other1.64
r_angle_refined_deg1.383
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.573
r_dihedral_angle_3_deg15.896
r_dihedral_angle_4_deg13.058
r_dihedral_angle_1_deg11.004
r_long_range_B_refined4.911
r_long_range_B_other4.911
r_mcangle_it2.059
r_mcangle_other2.059
r_scangle_other1.64
r_angle_refined_deg1.383
r_mcbond_it1.104
r_mcbond_other1.104
r_angle_other_deg0.951
r_scbond_it0.846
r_scbond_other0.846
r_chiral_restr0.079
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
Dynamic microtubule in GDP state
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 Particles48097
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise8.754
Angular Rotation-25.766
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 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)1.4
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 CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification27500
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONGctf
MODEL FITTINGUCSF Chimera
INITIAL EULER ASSIGNMENTEMAN
FINAL EULER ASSIGNMENTFREALIGN
RECONSTRUCTIONFREALIGN
MODEL REFINEMENTREFMAC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION