EMD-5625
Architecture of a helicase loading intermediate containing ORC-Cdc6-Cdt1-MCM2-7 on DNA reveals similarity to DNA polymerase clamp loading complexes
EMD-5625
Single-particle14.0 Å
Deposition: 04/04/2013Map released: 24/07/2013
Last modified: 14/08/2013
Concentration: 0.1
mg/mL
Buffer
pH: 7.5
Details: 50 mM HEPES-KOH
Details: 50 mM HEPES-KOH
Grid
Details: Thin carbon layer on holey carbon, glow discharged
Vitrification
Cryogen name: ETHANE
Chamber humidity: 70%
Instrument: FEI VITROBOT MARK I
Method: A thin carbon layer was floated onto holey carbon and glow discharged. 2.8 uL sample was added and after 30 seconds was blotted for 5 seconds and plunge-frozen.
Chamber humidity: 70%
Instrument: FEI VITROBOT MARK I
Method: A thin carbon layer was floated onto holey carbon and glow discharged. 2.8 uL sample was added and after 30 seconds was blotted for 5 seconds and plunge-frozen.
Microscope: JEOL 2010F
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2 mm
Nominal defocus: 1.2 µm - 4.4 µm
Nominal magnification: 60000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Liquid nitrogen cooled
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 400K magnification., Electron beam tilt params: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2 mm
Nominal defocus: 1.2 µm - 4.4 µm
Nominal magnification: 60000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Liquid nitrogen cooled
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 400K magnification., Electron beam tilt params: )
Image Recording
[1]
Detector category:
FILM
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Scanner: NIKON SUPER COOLSCAN 9000
Number of real images: 800
Average electron dose per image: 15 e/Å2
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Scanner: NIKON SUPER COOLSCAN 9000
Number of real images: 800
Average electron dose per image: 15 e/Å2
Details: Particles were selected with e2boxer.py in swarm mode. Additional good particles were selected and bad particles were removed manually. After structural factor and CTF correction in EMAN1, the phase-flipped particles were normalized (edgenorm, hp=1) and pooled. Refine2d.py was run and particles in bad class averages were removed. Initial models were made using EMAN2, but 3D refinement was performed using EMAN1.8 without ctfc or ctfcw.
Final
reconstruction
Resolution: 14.0
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 92049
Algorithm: OTHER
Details:
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 92049
Algorithm: OTHER
Details:
⌯ Applied Symmetry
Point group:
C1
Software
[1]
| Name | Version | Details |
|---|---|---|
| EMAN1, EMAN2 | - | - |
Final 2D classification
Number of classes:
1104
CTF correction
Details: Each particle set by ctfit
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of ORC-Cdc6-Cdt1-Mcm2-7 complex at DNA origin in ATPrS
Details: ::::EMDATABANK.org::::EMD-5625::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Reconstruction of ORC-Cdc6-Cdt1-Mcm2-7 complex at DNA origin in ATPrS
Details: ::::EMDATABANK.org::::EMD-5625::::
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Origin | -28 | -28 | -28 |
| Dimensions (px) | 56 | 56 | 56 |
| Dimensions (Å) | 236.88 | 236.88 | 236.88 |
| Voxel size (Å) | 4.23 | 4.23 | 4.23 |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 1.0 | AUTHOR |