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Map Challenge Targets

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

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EMD-6287

EMD-2788

EMD-5778

EMD-2660

EMD-6000

EMD-5995

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

RCSB-PDB / PDBe / PDBj

 1yar

RCSB-PDB / PDBe / PDBj

4v1w

RCSB-PDB / PDBe / PDBj

 3j5p

RCSB-PDB / PDBe / PDBj

3j79/3j7a

RCSB PDB: LS, SS PDBe: LS, SS PDBj: LS, SS

3j7l

RCSB-PDB / PDBe / PDBj

5a1a

RCSB-PDB / PDBe / PDBj

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

EMPIAR-10029

EMPIAR-10025

EMPIAR-10026

EMPIAR-10005

EMPIAR-10028

EMPIAR-10010 FAQ
EMPIAR-10011

EMPIAR-10013 EMPIAR-10012

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

 

10025.emx

10025.py

10026.emx

10026.py

10005.emx

10005.py

10028.emx

10028.py

10011.emx

10011.py

10013.emx

10013.py

Imposed Symmetry

Dihedral (D7)

None (C1)

FAQ

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-2) 50 53 16 41  20 52 45
dose per frame (e-2) -- 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

EMDataBank Validation Challenges are supported by NIH National Institute of General Medical Sciences

Please send your challenge questions, comments and feedback to challenges@emdatabank.org

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