Experiment: 11RL

CryoEM structure of the human origin recognition complex with DNA and CDC6 protein

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7JPS

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.241
f_angle_d	0.461
f_chiral_restr	0.037
f_plane_restr	0.004
f_bond_d	0.002

Sample
Human ORC subunits (1-5) and Human CDC6 protein complex with 60bp DNA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	The sample was applied to a glow-discharged Quantifoil R 0.6/1 300 mesh copper grid (previously washed with ethyl acetate), incubated for 10 seconds, ...	The sample was applied to a glow-discharged Quantifoil R 0.6/1 300 mesh copper grid (previously washed with ethyl acetate), incubated for 10 seconds, blotted for 3 seconds, and plunged into liquid ethane using a Leica Automatic Plunge Freezer EM GP2.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	130819
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.5 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (7JPS)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Initial local fitting was done using Chimera, and then Coot was used for flexible fitting and model building.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	43.2

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Warp	1.0.9
PARTICLE SELECTION	cryoSPARC	4.7.1
IMAGE ACQUISITION	Warp	1.0.9
IMAGE ACQUISITION	EPU
CTF CORRECTION	Warp	1.0.9
MODEL FITTING	Coot	0.9.8.95
INITIAL EULER ASSIGNMENT	cryoSPARC	4.7.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.7.1
CLASSIFICATION	cryoSPARC	4.7.1
RECONSTRUCTION	cryoSPARC	4.7.1
MODEL REFINEMENT	PHENIX	1.21.2_5419

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTF correction was done first in WARP during exposure/micrograph pre-processing, and re-corrected during the final refinements/reconstruction of the map in cryoSPARC		Particle picking used a BoxNet pre-trained neural network implemented in TensorFlow, with a particle diameter of 180 angstrom and a threshold score of 0.5