Login | ![]() |
![]() |
Six challenge targets are based on recently described 3DEM single particle structure determinations with data collected as multiple-frames-per-second movies, using the latest generation of detectors. One additional target is based on simulated (in silico) images. For each experimental target, the original raw micrograph movie frames are data available for download at EMPIAR, PDBe's raw 3DEM image data archive. Summed image data are also available, either as full micrographs or as picked particle stacks. In one case aligned frames are also deposited. Particle positions and defocus values from the raw data depositors are also available for download and may optionally be used by challengers in their reconstructions.
target | 1. GroEL in silico | 2. T20S Proteasome | 3. Apo-Ferritin | 4. TRPV1 Channel | 5. 80S Ribosome | 6. Brome Mosaic Virus | 7. β-Galactosidase |
Reference EMDB map entry |
-- |
|
|
|
|
|
|
Primary Citation | Vulovic et al | Campbell et al | Russo & Passmore | Liao et al | Wong et al | Wang et al | Bartesaghi et al |
Reported Resolution (Å) | ~3 | 2.8 | 4.7 | 3.3 | 3.2 | 3.8 | 3.2 |
Reference Model PDB entry |
4hel |
1yar |
4v1w |
3j5p |
3j79/3j7a |
3j7l |
5a1a |
Benchmark Storage Size |
2 GB |
2000 GB |
181 GB |
6300 GB |
2000 GB |
460 GB |
550 GB |
EMPIAR ID(s) data can also be downloaded from Chinese Academy of Sciences |
|||||||
Raw Frames |
n.a. | ✔ | ✔ | ✔ | ✔ | ✔ | ✔ |
Aligned Frames | ✔ | ||||||
Summed Micrographs |
✔ | ✔ | ✔ | ✔ | |||
Summed Particle Stacks | ✔ | ✔ | ✔ | ✔ | |||
Initial Particle Coordinates (directory link) |
spider FAQ | eman-box | eman-box | ||||
Final Particle Coordinates (direct file link) |
relion-star | relion-star | relion-star | ||||
Particle coordinates in EMX format; python script used for conversion files contributed by Roberto Marabini and Jose Maria Carazo |
|||||||
Imposed Symmetry |
Dihedral (D7) None (C1) |
Dihedral (D7) | Octahedral (O) | Cyclic (C4) | None (C1) | Icosahedral (I) | Dihedral (D2) |
Sample MW (MDa) | 0.8 | 0.7 | 0.44 | 0.3 | 4.2 | 4.6 | 0.47 |
Unique MW (kDa) | 57 | 50 | 20 | 80 | 4200 | 80 | 120 |
Microscope | -- | Titan Krios | Polara 300 | Polara 300 | Polara 300 | JEOL3200FSC | Titan Krios |
Voltage(kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
Cs (mm) |
2.7 | 2.7 | 2.7 FAQ | 2.0 | 2.0 | 4.1 | 2.7 |
Detector | Falcon I | K2 | Falcon II | K2 | Falcon II | DE12 | K2 |
Frame Sampling (Å/pixel) | 1.42 | 0.6575 | 1.346 | 1.22 FAQ | 1.34 | 0.99 | 0.64 |
total dose (e-/Å2) | 50 | 53 | 16 | 41 | 20 | 52 | 45 |
dose per frame (e-/Å2) | -- | 1.4 | 0.95 | 1.37 | 1 | 1.4 | 1.2 |
frame rate (f/s) | -- | 5 | 17 | 5 | 16 | 25 | 2.5 |
frame alignment method | -- | UCSF | not performed | UCSF | Statistical | DE script | cross-correlation script |
Particle selection method | -- | Appion-FindEM | EMAN2 | SamViewer | EMAN2 | EMAN2 | Gaussian correlation |
Number of Particles | 10000 | 49954 | 483 | 35645 | 105247 | 30000 | 11726 |
Particle/Map Sampling (Å/pixel) | 1.42 | 0.98 | 1.346 | 1.22 | 1.34 | 0.99 | 0.64 |
Raw Data Contributors (Thank You!) | Yuchen Deng, Fei Sun | Melody Campbell, Bridget Carragher | Chris Russo, Lori Passmore | Jean-Paul Armache, Maofu Liao, Yifan Cheng | Xiaochen Bai, Sjors Scheres | Zhao Wang, Wah Chiu | Alberto Bartesaghi, Sriram Subramaniam |
EMDataResource Validation Challenges are supported by NIH National Institute of General Medical Sciences
Please send your challenge questions, comments and feedback to challenges@emdataresource.org
Theme by Danetsoft and Danang Probo Sayekti inspired by Maksimer