9TH8 | pdb_00009th8

Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PT6
experimental model	PDB	7P30
experimental model	PDB	5BK4

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.779
f_angle_d	0.71
f_chiral_restr	0.045
f_plane_restr	0.005
f_bond_d	0.003

Sample
MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Wait time: 30 s Blotting time: 1.5 s Blot force: +2

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	292336
Reported Resolution (Å)	2.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details	For the composite MSC map, resolution was estimated with phenix.mtriage, using the unmasked model-map FSC, which gave an FSC(0.143) resolution of 2.9 ...	For the composite MSC map, resolution was estimated with phenix.mtriage, using the unmasked model-map FSC, which gave an FSC(0.143) resolution of 2.9 Angstrom. Final focused refinement particle subsets used to generate composite map (292,336 particles): DH core (38,859 particles) Sld3 MRD1/2:Mcm4/6 (149,668 particles) Sld3-Cdc45:Mcm2/5 (52,475 particles) Sld7:Mcm6 (51,334 particles)
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (7PT6, 7P30, 5BK4, 3WI3, 3X38, 6U0M)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	58.4	62.1

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3500
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	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Topaz
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4.1.14
INITIAL EULER ASSIGNMENT	RELION	4.0
FINAL EULER ASSIGNMENT	cryoSPARC	4.6.2
CLASSIFICATION	cryoSPARC	4.6.2
RECONSTRUCTION	cryoSPARC	4.6.2
RECONSTRUCTION	RELION	4.0
RECONSTRUCTION	PHENIX	1.21.2-5419
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