Happy Holidays and New year from the EMDB! Please be advised that the EMDB team will be operating at reduced capacity between December 15th - January 12th. With this in mind we would ask that you be prepared for longer reply times through both our helpdesk system and the OneDep deposition system. well done on a productive 2025, wishing you all the best and we will see you in 2026!

Resources

EM validation services

    • Fourier Shell Correlation (FSC) server
    • Tilt-pair validation server

Test Data

2D picked particle sets

Name Description Image size Voxel size Format
Birkbeck_GroEL_MDH_MODEL 3 stacks of 2781 model images each with different SNR 256x256 1.4Å CCP4
Birkbeck_GroEL_MDH_REAL 2781 CTF-corrected GroEL-MDF images 160x160 2.8Å Spider
SPIDER_FRANK_data 70S E. coli ribosome with (image 1-5000) and without (images 5001-10000) Elongation factor G (EF-G) provided by Haixiao Gao and J Frank. 130x130 2.82Å Spider


PDBeShape

Name Description Format Size
PDBeShape test set 200 entries of eukaryotic ribosomes, prokaryotic ribosomes, chaperonines, and viruses Tar 27 Gb


Pairs of 3D volumes for testing FSC server

Test case Voxel size Map 1 Map 2 Result
GroEL dataset publicly available
(Stagg et al., J. Struct. Biol. 163:29-39, 2008)		 1.63 Å 14 MB (MRC format) download 14 MB (MRC format) download View FSC plot

Datasets for testing Tilt-pair validation server

Parameter Icosahedral Bacillus stearothermophilus pyruvate dehydrogenase E2 core, 1.5 MDa, Rosenthal and Henderson, 2003 Chicken anemia virus (CAV), 2.7 MDa, Crowther et al., 2003 ß-galactosidase, 450 kDa, Chen et al., 2013
Map e2map.mrc cav_3d.mrc Bgal_3d.mrc
Untilted stack stack1.mrc cav6216_stk.mrc Bgal_untilt_stk.mrc
Parameters stack1.par cav6216.par Bgal_untilt.par
Parameter file type Frealign Frealign Frealign
Tilted stack stack2.mrc cav6217_stk.mrc Bgal_tilt_stk.mrc
Voxel size 4.98 Å 3.62 Å 2.98 Å
Mask radius 20 pixels 24 pixels 30 pixels
Tilt range (-20°, 20°) (-30°, 30°) (-20°, 20°)
Resolution range (100 Å, 15 Å) (100 Å, 25 Å) (150 Å, 35 Å)
Voltage 300 300 80
Defocus 59000 29000 31500
Spherical aberration 2 mm 2 mm 2 mm
Amplitude contrast 0.07 0 0
Results View View View