The Convergence Server

About this server

Briefly, 100 models are generated from the deposited atomic model and EM density using Rosetta, and the resulting models are sorted by Rosetta score, clash score, Ramachandran outliers, and MolProbity score. The top 10 scoring atomic models are refined into the EM density using Phenix real-space refinement and RMSDs of the Cαs are calculated. Regions of well-ordered electron microscopy density will show convergence between models (low RMSD), worse ordered density will have higher RMSD values.

No helical or nucleic-acid-containing complexes have been processed yet... we're working on it.

More details here:
http://biorxiv.org/content/early/2017/04/19/128561

Processed Entries

Disclaimer: Refinements and analyses are performed automatically, without user intervention. The results have not been individually assessed or inspected for accuracy. If you notice errors in a processed entry, let us know so that we can improve our pipeline.

sort by resolution

EMD-1641 - S. enterica serovar Typhimurium L-type flagella filament (4 Å res)
EMD-2677 - human gamma-secretase (4.5 Å res)
EMD-2857 - Dynactin complex from pig brain (3.5 Å res)
EMD-2924 - Recombinant human APC/C-Cdh1-Emi1 ternary complex (3.6 Å res)
EMD-2974 - T4-lysozyme fusion gamma-secretase (4.4 Å res)
EMD-2981 - human 20S proteasome core (3.5 Å res)
EMD-2984 - Escherichia coli beta-galactosidase bound to phenylethyl beta-D-thiogalactopyranoside (PETG) (2.2 Å res)
EMD-3061 - human gamma-secretase (3.4 Å res)
EMD-3062 - chicken Slo2.2 (4.5 Å res)
EMD-3063 - chicken Slo2.2 (4.2 Å res)
EMD-3121 - PGT128 Fab bound to BG505 SOSIP.664 HIV-1 Env trimer (4.36 Å res)
EMD-3179 - S.cerevisiae apo RNA polymerase III (closed clamp conformation) (4.6 Å res)
EMD-3180 - S.cerevisiae apo RNA polymerase III (open clamp conformation) (4.7 Å res)
EMD-3231 - Plasmodium falciparum 20S proteasome core bound to a specific inhibitor (3.6 Å res)
EMD-3237 - human gamma secretase in complex with a drug DAPT (4.2 Å res)
EMD-3238 - human gamma secretase in class 1 of the apo-state ensemble (4.1 Å res)
EMD-3239 - human gamma secretase in class 2 of the apo-state ensemble (4 Å res)
EMD-3295 - Full-length human p97 bound to UPCDC30245 inhibitor (2.3 Å res)
EMD-3296 - Full-length human p97 (2.4 Å res)
EMD-3297 - Full-length human p97 bound to ATPgS (3.3 Å res)
EMD-3298 - Full-length human p97 bound to ATPgS (3.2 Å res)
EMD-3299 - Full-length human p97 bound to ATPgS (3.3 Å res)
EMD-3308 - Cleaved JR-FL EnvdCT in complex with PGT151 Fab (4.19 Å res)
EMD-3309 - Cleaved JR-FL EnvdCT in complex with PGT151 Fab (4.30 Å res)
EMD-3338 - Complex of Human Hsp90 beta, human Cdc37 and human Cdk4 (4.0 Å res)
EMD-3353 - NMDA Receptor (5 Å res)
EMD-3366 - Exosome-Ski7 complex (4.2 Å res)
EMD-3385 - Recombinant human APC/C-Cdc20-Hsl1 complex (3.9 Å res)
EMD-3388 - Recombinant human apo APC/C phosphorylated in vitro (3.4 Å res)
EMD-3460 - RecBCD complex bound to inhibitory protein lambda GamS (3.8 Å res)
EMD-3488 - Haemoglobin (3.2 Å res)
EMD-3523 - Polycystin-2 (4.3 Å res)
EMD-3524 - Polycystin-2 (4.2 Å res)
EMD-3583 - Caenorhabditis elegans Separase-Securin complex (3.8 Å res)
EMD-3595 - Retinoschisin (4.2 Å res)
EMD-3602 - KaiCBA circadian clock complex (4.7 Å res)
EMD-3777 - ClpB homo hexamer, BAP form, double walker B mutant, in the ATPgammaS state (4.6 Å res)
EMD-4015 - Human immunodeficiency virus 1 (3.9 Å res)
EMD-4032 - Bovine respiratory Complex I (4.35 Å res)
EMD-4038 - Ternary complex of RecBCD with forked DNA substrate and ADPNP (3.83 Å res)
EMD-4040 - Bovine respiratory Complex I (4.27 Å res)
EMD-4061 - BAM complex (4.9 Å res)
EMD-4068 - Structure of TcdA1 in pore state, determined in lipid nanodisc (3.46 Å res)
EMD-4077 - 30S-IF1-IF3-mRNA-tRNA pre-initiation complex (state-2B) (4.45 Å res)
EMD-4080 - 30S-IF1-IF3-mRNA-tRNA pre-initiation complex (state-4) (4.0 Å res)
EMD-4088 - S. cerevisiae RNA polymerase I in the monomeric state (4.9 Å res)
EMD-5391 - rATcpn-alpha in apo state (4.9 Å res)
EMD-5623 - Thermoplasma acidophilum 20S proteasome (3.3 Å res)
EMD-5776 - Rat TRPV1 in complex with DkTx and resiniferatoxin (3.8 Å res)
EMD-5777 - Rat TRPV1 in complex with capsaicin (4.2 Å res)
EMD-5778 - Rat TRPV1 (3.275 Å res)
EMD-5995 - Escherichia coli beta-galactosidase (3.2 Å res)
EMD-6204 - ATP-bound N-ethylmaleimide sensitive factor (4.2 Å res)
EMD-6219 - T. acidophilum 20S proteasome (4.8 Å res)
EMD-6225 - Heptamer of C-terminal 63-kDa fragment of anthrax toxin protective antigen, pore conformation (3.6 Å res)
EMD-6239 - VP2 of Bluetongue Virus (3.3 Å res)
EMD-6240 - VP5 of Bluetongue Virus (3.3 Å res)
EMD-6267 - Recombinant human TRPA1 treated with AITC (4.24 Å res)
EMD-6272 - 13-fold average of VP6 trimer from full rotavirus reconstruction (2.6 Å res)
EMD-6287 - T20S Proteasome (2.8 Å res)
EMD-6324 - T4 portal protein gp20 (3.6 Å res)
EMD-6337 - VSV-L (3.8 Å res)
EMD-6338 - Eukaryotic Minichromosome Maintenance Complex (MCM2-7) (3.8 Å res)
EMD-6343 - Piezo-type mechanosensitive ion channel component 1 (4.8 Å res)
EMD-6344 - Zebra fish alpha-1 glycine receptor bound with strychnine (3.9 Å res)
EMD-6345 - Zebra fish alpha-1 glycine receptor bound with glycine (3.9 Å res)
EMD-6346 - Zebra fish alpha-1 glycine receptor bound with glycine/ivermectin (3.8 Å res)
EMD-6369 - Inositol 1,4,5-trisphosphate receptor, type 1 (4.7 Å res)
EMD-6408 - CPV VP4 + polymerase complex (TEC) (3.3 Å res)
EMD-6425 - Mature retinoschisin with a C-terminal hexahistidine tag (4.1 Å res)
EMD-6455 - Rabbit TRPV2 (3.8 Å res)
EMD-6458 - NAIP2/NLRC4 inflammasome, 11-fold disk (4.7 Å res)
EMD-6475 - a membrane protein cryo-sample (4.2 Å res)
EMD-6478 - Saccharomyces cerevisiae large 60S ribosomal subunit (2.9 Å res)
EMD-6479 - Recombinant yeast 26S proteasome lid complex (3.5 Å res)
EMD-6480 - Heptameric apoptosome of activated human Apaf-1 binding to horse cytochrome c and dATP (3.8 Å res)
EMD-6481 - Heptameric apoptosome of activated human Apaf-1 binding to horse cytochrome c and dATP (4.4 Å res)
EMD-6526 - Murine hepatitis virus protein S (4.0 Å res)
EMD-6534 - Saccharomyces cerevisiae CMG complex (3.7 Å res)
EMD-6535 - Saccharomyces cerevisiae CMG complex (4.7 Å res)
EMD-6536 - Saccharomyces cerevisiae CMG complex (4.8 Å res)
EMD-6551 - CorA from Thermotoga maritima in the presence of magnesium (3.8 Å res)
EMD-6580 - Recombinant rat full-length TRPV2 (4.4 Å res)
EMD-6617 - Spinach PSII-LHCII supercomplex (3.2 Å res)
EMD-6630 - Glutamate dehydrogenase, unliganded (apo) form (3.26 Å res)
EMD-6631 - Binary complex of bovine glutamate dehydrogenase with GTP (3.47 Å res)
EMD-6632 - Ternary complex of bovine glutamate dehydrogenase with GTP and NADH (3.6 Å res)
EMD-6633 - Ternary complex of bovine glutamate dehydrogenase with GTP and NADH (3.4 Å res)
EMD-6634 - Binary complex of bovine glutamate dehydrogenase with NADH (3.3 Å res)
EMD-6635 - Binary complex of bovine glutamate dehydrogenase with NADH (3.3 Å res)
EMD-6640 - NPC1 (4.43 Å res)
EMD-6656 - Cyclic nucleotide-gated (CNG) channels (3.5 Å res)
EMD-6668 - human mTOR complex 1 (4.4 Å res)
EMD-6675 - Full length T2SS secretin GspD complex (3.04 Å res)
EMD-6676 - Full length T2SS secretin GspD in Vibrio cholerae (3.26 Å res)
EMD-6677 - Full length T2SS secretin GspD G453A mutant in Vibrio cholerae (4.22 Å res)
EMD-6698 - voltage-gated sodium channel (3.8 Å res)
EMD-6703 - SARS-CoV spike trimer (3.2 Å res)
EMD-6704 - MERS-CoV spike trimer (3.2 Å res)
EMD-6705 - SARS-CoV spike trimer (3.2 Å res)
EMD-6706 - MERS-CoV spike trimer (3.2 Å res)
EMD-6707 - MERS-CoV spike trimer (3.2 Å res)
EMD-8015 - Membrane-inserted form of the nonameric pore forming protein Lysenin (3.1 Å res)
EMD-8069 - HKU1 spike with attached foldon domain and mutated furin-cleavage site (4.04 Å res)
EMD-8072 - alcohol oxidase (3.37 Å res)
EMD-8117 - TRPV1 ion channel in complex with DkTx and RTX (2.95 Å res)
EMD-8118 - TRPV1 ion channel in unliganded state (3.28 Å res)
EMD-8119 - TRPV1 ion channel in complex with capsazepine (3.43 Å res)
EMD-8162 - F-actin-tropomyosin complex (3.6 Å res)
EMD-8163 - F-actin-tropomyosin complex (3.6 Å res)
EMD-8164 - F-actin-myosin-tropomyosin complex (3.9 Å res)
EMD-8165 - F-actin-myosin-tropomyosin complex (3.9 Å res)
EMD-8185 - aerolysin prepore (3.9 Å res)
EMD-8188 - aerolysin post-prepore and quasipore (4.46 Å res)
EMD-8191 - Lactate dehydrogenase (LDH) in complex with GSK2837808A (2.8 Å res)
EMD-8192 - isocitrate dehydrogenase R132C mutant (3.8 Å res)
EMD-8193 - Isocitrate dehydrogenase R132C mutant in complex with ML309 (3.8 Å res)
EMD-8194 - Glutamate dehydrogenase (1.8 Å res)
EMD-8200 - Polycystin-2 channel t (4.22 Å res)
EMD-8215 - Voltage-gated K+ channel Eag1 bound to the channel inhibitor calmodulin (3.78 Å res)
EMD-8240 - Ebola virus trimeric surface glycoprotein in complex with IgG c2G4 and c13C6 Fabs (4.3 Å res)
EMD-8242 - Ebola virus trimeric surface glycoprotein in complex with IgG c4G7 and c13C6 Fabs (4.3 Å res)
EMD-8289 - GluK2EM with 2S,4R-4-methylglutamate (3.8 Å res)
EMD-8315 - Complex of zebrafish (D. rerio) STRA6 with copurified calmodulin reconstituted in amphipol A8-35 (3.9 Å res)
EMD-8331 - Human coronavirus NL63 spike glycoprotein ectodomain (3.4 Å res)
EMD-8354 - hPKD:198-703 (3.0 Å res)
EMD-8399 - Type III injectisome basal body (3.6 Å res)
EMD-8409 - Vo region of the V-ATPase from Saccharomyces cerevisiae (3.9 Å res)
EMD-8414 - Ca2+ bound aplysia Slo1 (3.8 Å res)
EMD-8454 - A bovine CLC-K channel complexed with a monoclonal antibody fragment (Fab) (3.95 Å res)
EMD-8461 - Cystic fibrosis transmembrane conductance regulator or ABCC7 (3.73 Å res)
EMD-8479 - Mediator complex (4.4 Å res)
EMD-8481 - complex formed by a tetrameric assembly of Sso7d-fusion HIV-1 Integrase with the product of DNA strand transfer (3.9 Å res)
EMD-8482 - TAP ATP-Binding Cassette Transporter (3.97 Å res)
EMD-8511 - Human HCN1 hyperpolarization-activated cyclic nucleotide-gated ion channel (3.5 Å res)
EMD-8512 - Human HCN1 hyperpolarization-activated cyclic nucleotide-gated ion channel in complex with cAMP (3.51 Å res)
EMD-8516 - Cystic fibrosis transmembrane conductance regulator or ABCC7 (3.87 Å res)
EMD-8559 - bovine multidrug resistance protein 1 (MRP1) (3.49 Å res)
EMD-8560 - bovine multidrug resistance protein 1 (MRP1) complexed with leukotriene C4 (3.34 Å res)
EMD-8608 - homo hexamer of PqiB (3.96 Å res)
EMD-8623 - Complex of a full-length, active-state calcitonin receptor with peptide ligand, heterotrimeric Gs protein and nano body 35. (4.1 Å res)
EMD-8632 - LliK (4.2 Å res)
EMD-8643 - BG505 SOSIP.664 trimer in complex with PGT145 and 3BNC117 Fabs (4.3 Å res)
EMD-8650 - human ether-a-go-go related K+ channel hERG (3.7 Å res)
EMD-8651 - human ether-a-go-go related K+ channel hERG (3.8 Å res)
EMD-8652 - human ether-a-go-go related K+ channel hERG (4.0 Å res)
EMD-9513 - voltage-gated calcium channel Cav1.1 (3.6 Å res)
EMD-9514 - voltage-gated calcium channel Cav1.1 (3.9 Å res)
EMD-9515 - voltage-gated calcium channel Cav1.1 (3.9 Å res)
EMD-9535 - PaeCas3-AcrF3 complex (4.5 Å res)
EMD-9540 - Yeast NPP-TRiC (4.7 Å res)
EMD-9541 - Yeast TRiC-AMP-PNP (4.6 Å res)
EMD-9570 - INX-6 (3.3 Å res)
EMD-9571 - INX-6 (3.6 Å res)

Plots

Click on a point to visit the summary page for that entry

Average RMSD & Reported Resolution

EMD-1641 EMD-2677 EMD-2857 EMD-2924 EMD-2974 EMD-2981 EMD-2984 EMD-3061 EMD-3062 EMD-3063 EMD-3121 EMD-3179 EMD-3180 EMD-3231 EMD-3237 EMD-3238 EMD-3239 EMD-3295 EMD-3296 EMD-3297 EMD-3298 EMD-3299 EMD-3308 EMD-3309 EMD-3338 EMD-3353 EMD-3366 EMD-3385 EMD-3388 EMD-3460 EMD-3488 EMD-3523 EMD-3524 EMD-3583 EMD-3595 EMD-3602 EMD-3777 EMD-4015 EMD-4032 EMD-4038 EMD-4040 EMD-4061 EMD-4068 EMD-4077 EMD-4080 EMD-4088 EMD-5391 EMD-5623 EMD-5776 EMD-5777 EMD-5778 EMD-5995 EMD-6204 EMD-6219 EMD-6225 EMD-6239 EMD-6240 EMD-6267 EMD-6272 EMD-6287 EMD-6324 EMD-6337 EMD-6338 EMD-6343 EMD-6344 EMD-6345 EMD-6346 EMD-6369 EMD-6408 EMD-6425 EMD-6455 EMD-6458 EMD-6475 EMD-6478 EMD-6479 EMD-6480 EMD-6481 EMD-6526 EMD-6534 EMD-6535 EMD-6536 EMD-6551 EMD-6580 EMD-6617 EMD-6630 EMD-6631 EMD-6632 EMD-6633 EMD-6634 EMD-6635 EMD-6640 EMD-6656 EMD-6668 EMD-6675 EMD-6676 EMD-6677 EMD-6698 EMD-6703 EMD-6704 EMD-6705 EMD-6706 EMD-6707 EMD-8015 EMD-8069 EMD-8072 EMD-8117 EMD-8118 EMD-8119 EMD-8162 EMD-8163 EMD-8164 EMD-8165 EMD-8185 EMD-8188 EMD-8191 EMD-8192 EMD-8193 EMD-8194 EMD-8200 EMD-8215 EMD-8240 EMD-8242 EMD-8289 EMD-8315 EMD-8331 EMD-8354 EMD-8399 EMD-8409 EMD-8414 EMD-8454 EMD-8461 EMD-8479 EMD-8481 EMD-8482 EMD-8511 EMD-8512 EMD-8516 EMD-8559 EMD-8560 EMD-8608 EMD-8623 EMD-8632 EMD-8643 EMD-8650 EMD-8651 EMD-8652 EMD-9513 EMD-9514 EMD-9515 EMD-9535 EMD-9540 EMD-9541 EMD-9570 EMD-9571

EMRinger Score & Reported Resolution

http://fraserlab.com/2015/02/18/EMringer/

EMD-1641 EMD-2677 EMD-2924 EMD-2974 EMD-2981 EMD-2984 EMD-3061 EMD-3062 EMD-3063 EMD-3121 EMD-3179 EMD-3180 EMD-3231 EMD-3237 EMD-3238 EMD-3239 EMD-3295 EMD-3296 EMD-3297 EMD-3298 EMD-3299 EMD-3308 EMD-3309 EMD-3338 EMD-3366 EMD-3385 EMD-3388 EMD-3460 EMD-3488 EMD-3523 EMD-3524 EMD-3583 EMD-3595 EMD-4015 EMD-4032 EMD-4038 EMD-4040 EMD-4061 EMD-4068 EMD-4077 EMD-4080 EMD-4088 EMD-5391 EMD-5623 EMD-5776 EMD-5777 EMD-5778 EMD-5995 EMD-6204 EMD-6219 EMD-6225 EMD-6239 EMD-6240 EMD-6267 EMD-6272 EMD-6287 EMD-6324 EMD-6337 EMD-6338 EMD-6343 EMD-6344 EMD-6345 EMD-6346 EMD-6369 EMD-6408 EMD-6425 EMD-6455 EMD-6458 EMD-6475 EMD-6479 EMD-6480 EMD-6481 EMD-6526 EMD-6534 EMD-6535 EMD-6536 EMD-6551 EMD-6580 EMD-6630 EMD-6631 EMD-6632 EMD-6633 EMD-6634 EMD-6635 EMD-6640 EMD-6656 EMD-6668 EMD-6675 EMD-6676 EMD-6677 EMD-6698 EMD-6703 EMD-6704 EMD-6705 EMD-6706 EMD-6707 EMD-8015 EMD-8069 EMD-8072 EMD-8117 EMD-8118 EMD-8119 EMD-8162 EMD-8163 EMD-8164 EMD-8165 EMD-8185 EMD-8188 EMD-8191 EMD-8192 EMD-8193 EMD-8194 EMD-8200 EMD-8215 EMD-8240 EMD-8242 EMD-8289 EMD-8315 EMD-8331 EMD-8354 EMD-8399 EMD-8409 EMD-8414 EMD-8454 EMD-8461 EMD-8479 EMD-8482 EMD-8511 EMD-8512 EMD-8516 EMD-8559 EMD-8560 EMD-8608 EMD-8623 EMD-8632 EMD-8643 EMD-8650 EMD-8651 EMD-8652 EMD-9513 EMD-9514 EMD-9515 EMD-9535 EMD-9540 EMD-9541 EMD-9570 EMD-9571

EMRinger Score & Average RMSD

EMD-1641 EMD-2677 EMD-2924 EMD-2974 EMD-2981 EMD-2984 EMD-3061 EMD-3062 EMD-3063 EMD-3121 EMD-3179 EMD-3180 EMD-3231 EMD-3237 EMD-3238 EMD-3239 EMD-3295 EMD-3296 EMD-3297 EMD-3298 EMD-3299 EMD-3308 EMD-3309 EMD-3338 EMD-3366 EMD-3385 EMD-3388 EMD-3460 EMD-3488 EMD-3523 EMD-3524 EMD-3583 EMD-3595 EMD-4015 EMD-4032 EMD-4038 EMD-4040 EMD-4061 EMD-4068 EMD-4077 EMD-4080 EMD-4088 EMD-5391 EMD-5623 EMD-5776 EMD-5777 EMD-5778 EMD-5995 EMD-6204 EMD-6219 EMD-6225 EMD-6239 EMD-6240 EMD-6267 EMD-6272 EMD-6287 EMD-6324 EMD-6337 EMD-6338 EMD-6343 EMD-6344 EMD-6345 EMD-6346 EMD-6369 EMD-6408 EMD-6425 EMD-6455 EMD-6458 EMD-6475 EMD-6479 EMD-6480 EMD-6481 EMD-6526 EMD-6534 EMD-6535 EMD-6536 EMD-6551 EMD-6580 EMD-6630 EMD-6631 EMD-6632 EMD-6633 EMD-6634 EMD-6635 EMD-6640 EMD-6656 EMD-6668 EMD-6675 EMD-6676 EMD-6677 EMD-6698 EMD-6703 EMD-6704 EMD-6705 EMD-6706 EMD-6707 EMD-8015 EMD-8069 EMD-8072 EMD-8117 EMD-8118 EMD-8119 EMD-8162 EMD-8163 EMD-8164 EMD-8165 EMD-8185 EMD-8188 EMD-8191 EMD-8192 EMD-8193 EMD-8194 EMD-8200 EMD-8215 EMD-8240 EMD-8242 EMD-8289 EMD-8315 EMD-8331 EMD-8354 EMD-8399 EMD-8409 EMD-8414 EMD-8454 EMD-8461 EMD-8479 EMD-8482 EMD-8511 EMD-8512 EMD-8516 EMD-8559 EMD-8560 EMD-8608 EMD-8623 EMD-8632 EMD-8643 EMD-8650 EMD-8651 EMD-8652 EMD-9513 EMD-9514 EMD-9515 EMD-9535 EMD-9540 EMD-9541 EMD-9570 EMD-9571

Contact

Please send questions/comments/requests/hate mail to:

glander@scripps.edu