6FE8 | pdb_00006fe8

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

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VEQ
experimental model	PDB	1NEX

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	50.886
r_long_range_B_other	50.846
r_scangle_other	41.658
r_dihedral_angle_2_deg	30.625
r_mcangle_it	30.386
r_mcangle_other	30.384
r_scbond_it	26.289
r_scbond_other	26.287
r_mcbond_it	18.689
r_mcbond_other	18.683
r_dihedral_angle_4_deg	15.563
r_dihedral_angle_3_deg	15.126
r_dihedral_angle_1_deg	7.605
r_angle_other_deg	3.765
r_angle_refined_deg	2.25
r_chiral_restr	0.149
r_bond_refined_d	0.02
r_gen_planes_other	0.013
r_gen_planes_refined	0.009
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 State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	69392
Reported Resolution (Å)	4.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details	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 Type	POINT
Number of Particles	187606
Reported Resolution (Å)	3.7
Resolution Method	FSC 0.143 CUT-OFF
Other Details	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 Type	POINT
Point Symmetry	C1
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (2VEQ, 1NEX)
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	4.6	4.06

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification	47170
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Gautomatch
IMAGE ACQUISITION	EPU	1.9.1
CTF CORRECTION	CTFFIND	4.0
MODEL FITTING	UCSF Chimera	1.8.1
MODEL FITTING	Coot	0.8.8
MODEL REFINEMENT	PHENIX	1.13
MODEL REFINEMENT	REFMAC
INITIAL EULER ASSIGNMENT	RELION	2.0
FINAL EULER ASSIGNMENT	RELION	2.0
CLASSIFICATION	RELION	2.0
RECONSTRUCTION	RELION	2.0
PARTICLE SELECTION	Gautomatch
CTF CORRECTION	CTFFIND	4.0
INITIAL EULER ASSIGNMENT	RELION	2.0
FINAL EULER ASSIGNMENT	RELION	2.0
CLASSIFICATION	RELION	2.0
RECONSTRUCTION	RELION	2.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		139303
PHASE FLIPPING AND AMPLITUDE CORRECTION		289281