8TL6 | pdb_00008tl6

Cryo-EM structure of DDB1deltaB-DDA1-DCAF5

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Q0R
in silico model	RoseTTAFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.4492
f_angle_d	0.4723
f_chiral_restr	0.0455
f_plane_restr	0.0037
f_bond_d	0.0023

Sample
Complex of DDB1deltaB-DDA1-DCAF5

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	NITROGEN
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	547805
Reported Resolution (Å)	2.63
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6q0r, 6q0r)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value	97
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	53.349

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	2500
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	36000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Topaz	0.2.4
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC	v3.2
MODEL FITTING	UCSF ChimeraX	1.4
MODEL FITTING	Coot	0.9
INITIAL EULER ASSIGNMENT	cryoSPARC	v3.2
FINAL EULER ASSIGNMENT	cryoSPARC	v3.2
CLASSIFICATION	cryoSPARC	v3.2
RECONSTRUCTION	cryoSPARC	v4.1.2
MODEL REFINEMENT	PHENIX	1.19.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	implemented in cryoSPARCv3.2	1404938