6FE8 | pdb_00006fe8

Cryo-EM structure of the core Centromere Binding Factor 3 complex


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VEQ 
experimental modelPDB 1NEX 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined50.886
r_long_range_B_other50.846
r_scangle_other41.658
r_dihedral_angle_2_deg30.625
r_mcangle_it30.386
r_mcangle_other30.384
r_scbond_it26.289
r_scbond_other26.287
r_mcbond_it18.689
r_mcbond_other18.683
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined50.886
r_long_range_B_other50.846
r_scangle_other41.658
r_dihedral_angle_2_deg30.625
r_mcangle_it30.386
r_mcangle_other30.384
r_scbond_it26.289
r_scbond_other26.287
r_mcbond_it18.689
r_mcbond_other18.683
r_dihedral_angle_4_deg15.563
r_dihedral_angle_3_deg15.126
r_dihedral_angle_1_deg7.605
r_angle_other_deg3.765
r_angle_refined_deg2.25
r_chiral_restr0.149
r_bond_refined_d0.02
r_gen_planes_other0.013
r_gen_planes_refined0.009
r_bond_other_d
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
The core Centromere Binding Factor 3 complex
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK I
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles69392
Reported Resolution (Å)4.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details3D auto-refinement of all the good particles from 2D classification, provided a reconstruction at 4.7 angstrom overall resolution. After post-process ...3D auto-refinement of all the good particles from 2D classification, provided a reconstruction at 4.7 angstrom overall resolution. After post-process by RELION and sharpened by a negative B-factor using an automated procedure resulting in a 4.1 angstrom reconstruction.
Refinement Type
Symmetry TypePOINT
Number of Particles187606
Reported Resolution (Å)3.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details187, 606 particles were in the best two 3D classes. 3D auto-refinement of the 3D joined classes against the corresponding particles resulted in a fina ...187, 606 particles were in the best two 3D classes. 3D auto-refinement of the 3D joined classes against the corresponding particles resulted in a final reconstruction.
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (2VEQ, 1NEX)
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement TargetCross-correlation coefficient
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)4.64.06
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification47170
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONGautomatch
IMAGE ACQUISITIONEPU1.9.1
CTF CORRECTIONCTFFIND4.0
MODEL FITTINGUCSF Chimera1.8.1
MODEL FITTINGCoot0.8.8
MODEL REFINEMENTPHENIX1.13
MODEL REFINEMENTREFMAC
INITIAL EULER ASSIGNMENTRELION2.0
FINAL EULER ASSIGNMENTRELION2.0
CLASSIFICATIONRELION2.0
RECONSTRUCTIONRELION2.0
PARTICLE SELECTIONGautomatch
CTF CORRECTIONCTFFIND4.0
INITIAL EULER ASSIGNMENTRELION2.0
FINAL EULER ASSIGNMENTRELION2.0
CLASSIFICATIONRELION2.0
RECONSTRUCTIONRELION2.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION139303
PHASE FLIPPING AND AMPLITUDE CORRECTION289281