Happy Holidays & Happy New Year from the EMDB team! During this period (23rd December - 6th January) the EMDB team and our OneDep curators will be working at reduced capacity. We will continue to run the weekly release of entries as normal, but entry annotation & support may be slower than usual. Thanks for your understanding.
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 |
Quick links
Recent Entries
(Show all)In situ structure of the Helicobacter pylori flagellar motor from the deletion of fapH with full length pflA
Cryo-EM structure of the S. cerevisiae ORC-Cdc6-Mcm2-7-DNA complex with a fully closed Mcm2-Mcm5 DNA entry gate
Structure of the Salmonella flagellar MS-ring with C11 symmetry applied
Structure of chanoclavine synthase from Claviceps fusiformis in complex with prechanoclavine
Structure of the Argonaute protein from Kurthia massiliensis in complex with guide DNA and 19-mer target DNA in target-cleaved state
Cryo-EM structure of human TUT1 complexed with U6 snRNA (consensus map)
Cryo-EM structure of the 10-subunits Mmp1 complex from Mycobacterium smegmatis
Structure of the RBM3 ring of Salmonella flagellar MS-ring protein FliF with C34 symmetry applied
LH2 complex from Ectothiorhodospira haloalkaliphila at near-atomic resolution
Structure of the RBM3 ring of Salmonella flagellar MS-ring protein FliF with C33 symmetry applied
Structure of the Argonaute protein from Kurthia massiliensis in complex with guide DNA
Structure of the Argonaute protein from Kurthia massiliensis in complex with guide DNA and 19-mer target DNA
Bacterial flagellar sodium-driven stator PomA5PomB2(D24N) with 100 mM KCl
Structure of the 33-mer RBM3 ring of Salmonella flagellar MS-ring protein FliF with C1 symmetry applied
Structure of the 34-mer RBM3 ring of Salmonella flagellar MS-ring protein FliF with C1 symmetry applied
Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM NaCl
Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM NaCl and 0.1 mM phenamil
Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM KCl
Bacterial flagellar sodium-driven stator PomA5PomB2(D24N) with 100 mM NaCl
Cryo-EM structure of human TUT1 complexed with U6 snRNA (KA-1 focused map)
Structure of the Argonaute protein from Kurthia massiliensis in complex with guide DNA and 19-mer target DNA in target-released state
Cryo-EM structure of human TUT1 complexed with U6 snRNA (5'-RNA focused map)
Cryo-EM structure of Lactobacillus casei DdmE bound with guide and target
Cryo-EM structure of the N2-4N2C402 complex at a resolution of 1.9 angstrom
Cryo-EM structure of an MCM helicase single hexamer loaded onto dsDNA.
Cryo-EM structure of the molybdenum nitrogenase complexed with iron protein (NifH) and Shethna protein II (FeSII)
Beta-galactosidase (LacZ) in complex with galactosyrin from Pseudomonas syringae.
CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : LM32Cs1C1 mutant snoRNA overexpression, class 4