Strain, strain background (E. coli) | MegaX DH10B T1R | Thermo Fischer Scientific | C640003 | Cloning strain |
Strain, strain background (E. coli) | One Shot BL21 Star (DE3) | Thermo Fischer Scientific | C601003 | Expression strain |
Strain, strain background (Geobacillus stearothermophilus) | ATCC 7953 | ATCC | ATCC 7953 | |
Recombinant DNA reagent | pETDuet1 | EMD Millipore | 71146-3 | Expression vector |
Sequence-based reagent | Codon-optimized IMEF cargo protein gene + encapsulin capsid protein gene containing overhangs for Gibson Assembly (oligonucleotide gBlock) | Integrated DNA Technologies (IDT) | based on accessions: WP_039238473.1; WP_03923847 | gttaagtataagaaggagatatacaATGAAGGAAGAACTGGATGCTTTCCATCAGATTTTCACTACGACCAA AGAGGCAATCGAACGTTTTATGGCGATGCTGACCCCGGTCATTGAGAACGCGGAGGACGATCATGAGCGCCTGTATTATCATCATATCTACGAAGAGGAGGAGCAACGTCTGTCGCGCCTGGACGTTCTGATCCCACTGATCGAAAAGTTTCAAGATGAAACCGACGAAGGCCTCTTCTCCCCCTCCAACAACGCCTTTAACCGTCTGCTTCAGGAGCTGAATCTGGAAAAATTCGGTTTGCATAACTTTATCGAGCATGTTGACCTGGCCCTTTTTAGTTTCACCGACGAGGAACGCCAGACATTGCTTAAAGAACTGCGTAAAGATGCCTATGAAGGCTATCAGTATGTTAAAGAAAAACTGGCAGAAATTAACGCTCGTTTTGATCACGATTACGCAGACCCGCATGCGCACCATGATGAACACCGTGACCATCTTGCGGATATGCCCTCAGCGGGTTCATCGCACGAAGAAGTGCAGCCTGTTGCACATAAAAAGAAAGGTTTCACGGTGGGTTCATTAATCCAGTAAATTTCGCTTAAATATTACCGCTAGCTCAAAAAGGAGGAAAAGTGAATGAACAAAAGCCAACTTTATCCGGATTCACCACTGACGGATCAGGACTTCAACCAATTAGACCAAACCGTGATTGAGGCTGCTCGTCGTCAGCTGGTGGGTCGTCGCTTCATTGAGTTATATGGCCCATTGGGGCGTGG CATGCAGAGTGTCTTCAACGATATCTTCATGGAGTCTCATG AAGCGAAAATGGACTTCCAGGGCAGCTTTG ACACGGAGGTAGAGTCCTCCCGTCGTGTAAACTATACCATTCCGATGTTATATAAAGACTTCGTGCTTTACTGGCGCGATCTGGAACAGAGCAAGGCACTCGATATTCCGATCGACTTTTCAGTGGCAGCGAACGCTGCCCGCGACGTTGCGTTCCTGGAAGATCAGATGATTTTCCATGGAAGCAAAGAATTTGATATCCCGGGTCTGATGAACGTGAAAGGTCGCCTGACCCATCTGATTGGCAATTGGTATGAGTCGGGTAACGCCTTTCAGGATATTGTGGAGGCCCGCAATAAATTACTCGAAATGAACCACAATGGCCCATATGCTCTCGTGCTGTCCCCGGAGCTGTACTCACTCTTA CATCGTGTGCATAAAGACACGAATGTGCTGGAGATCGAACACGTGCGCGAGTTGATTACTGCTGGGGTTTTTCAGTCGCCTGTCCTCAAAGGGAAAAGTGGTGTGATCGTAAACACCGGTCGCAACAATCTGGATTTGGCTATCTCGGAAGATTTTGAGACTGCATACCTGGG CGAGGAAGGTATGAACCATCCCTTTCGCGTGTACGAGACAGTTGTTCTGCGCATCAAACGCCCGGCGGCCATTTGTACTTTAATCGATCCGGAAGAATAAattaacctaggctgctgccaccgct |
Sequence- based reagent | Codon-optimized IMEF cargo protein gene w/o TP + encapsulin capsid protein gene containing overhangs for Gibson Assembly (oligonucleotide gBlock) | Integrated DNA Technologies (IDT) | based on accessions: WP_039238473.1; WP_039238471 | gttaagtataagaaggagatatacaATGAAGGAAGAACTGGATGCTTTCCATCAGATTTTCACTACGACCAAAGAGGCAATCGAACGTTTTATGGCGATGCTGACCCCGGTCATTGAGAACGCGGAGGACGATCATGAGCGCCTGTATTATCATCATATCTACGAAGAGGAGGAGCAACGTCTGTCGCGCCTGGACGTTCTGATCCCACTGATCGAAAAGTTTCAAGATGAAACCGACGAAGGCCTCTTCTCCCCCTCCAACAACGCCTTTAACCGTCTGCTTCAGGAGCTGAATCTGGAAAAATTCGGTTTGCATAACTTTATCGAGCATGT TGACCTGGCCCTTTTTAGTTTCACCGACGAGGAACGCCAGACATTGCTTAAAGAACTGCGTAAAGATGCCTATGAAGGCTATCAGTATGTTAAAGAAAAACTGGCAGAAATTAACGCTCGTTTTGATCACGATTACGCAGACCCGCATGCGCACCATGATGAACACCGTGACCATCTTGCGGATATGCCCTCAGCGGGTTCATCGCACGAAGAAGTGCAGCCTGTTGCATAAATTTCGCTTAAATATTACCGCTAGCTCAAAAAGGAGGAAAAGTGAATGAACAAAAGCCAACTTTATCCGGATTCACCACTGACGGATCAGGACTTCAACCAATTAGACCAAACCGTGATTG AGGCTGCTCGTCGTCAGCTGGTGGGT CGTCGCTTCATTGAGTTATATGGCCCA TTGGGGCGTGGCATGCAGAGTGTCTTCAACGATATCTTCATGGAGTCTCATGAAGCGAAAATGGACTTCCAGGGC AGCTTTGACACGGAGGTAGAGTCCTCCCGTCGTGTAAACTATACCATTCCGATGTTATATAAAGACTTCGTGCTTTACTGGCGCGATCTGGAACAGAGCAAGGCACTCGATATTCCGATCGACTTTTCAGTGGCAGCGAACGCTGCCCGCGACGTTGCGTTCCTGGAAGATCAGATGATTTTCCATGGAAGCAAAGAATTTGATATCCCGGGTCT GATGAACGTGAAAGGTCGCCTGACCCATCTGATTGGCAATTGGTATGAG TCGGGTAACGCCTTTCAGGATATTG TGGAGGCCCGCAATAAATTACTCGAAATGAACCACAATGGCCCATATGCTCTCGTGCTGTCCCCGGAGCTGTACTCACT CTTACATCGTGTGCATAAAGACACGAATGTGCTGGAGATCGAACACGTGCGCGAGTTGATTACTGCTGGGGTTTTTCAGTCGCCTGTCCTCAAAGGGAAAAGTGGTGTGATCGTAAACACCGGTCGCAACAATCTGGATTTGGCTATCTCGGAAGATTTTGAGACTGCATACCTGGGCGAGGAAGGTATGAACCATCCCTTTCGCGTGTACGAGACAGTTGTTCTGCGCATCAAACGCCCGGCGGCCATTTGTACTTTAATCGATCCGGAAGAATAAattaacctaggctgctgccaccgct |
Commercial assay or kit | Gibson Assembly Master Mix | New England Biolabs | E2611L | |
Commercial assay or kit | 14% Novex Tris-Glycine Gel | Thermo Fischer Scientific | XP00140BOX | |
Commercial assay or kit | MIDAS screen | Molecular Dimensions | MD1–59 | Crystallization screen |
Commercial assay or kit | Pierce Coomassie Plus (Bradford) Assay | Thermo Fischer Scientific | 23236 | Protein concentration determination4 |
Chemical compound, drug | Isopropyl-β-D-thiogalactoside | Millipore Sigma | 10724815001 | |
Chemical compound, drug | Lysozyme | Millipore Sigma | L6876 | |
Chemical compound, drug | DNAse I | Millipore Sigma | 11284932001 | |
Chemical compound, drug | Ni-NTA agarose resin | Qiagen | 30210 | |
Chemical compound, drug | Polyethylene glycol 8000 | Millipore Sigma | 1546605 | |
Chemical compound, drug | Uranyl formate | EMS | 22450 | |
Chemical compound, drug | Formaldehyde 37% in water | Millipore Sigma | 252549 | |
Chemical compound, drug | Glutaraldehyde 25% in water | Millipore Sigma | G5882 | |
Chemical compound, drug | Picric acid | Millipore Sigma | 197378 | |
Chemical compound, drug | Sodium cacodylate | Millipore Sigma | C0250 | |
Chemical compound, drug | Uranyl acetate | EMS | 22400 | |
Chemical compound, drug | Propylene oxide | Millipore Sigma | 82320 | |
Chemical compound, drug | Epon | EMS | 14910 | |
Chemical compound, drug | Glycolic acid | Millipore Sigma | 798053 | |
Chemical compound, drug | Trisodium citrate | Millipore Sigma | S1804 | |
Chemical compound, drug | Ammonium iron (II) sulfate | Millipore Sigma | F1543 | |
Chemical compound, drug | ortho-phenylenediamine | Millipore Sigma | P9029 | |
Chemical compound, drug | Hydrogen peroxide 30 % in water | Millipore Sigma | 216763 | |
Software, algorithm | Genome Neighborhood Network Tool (GNT) | Gerlt et al., 2015 | https://efi.igb.illinois.edu/efi-gnt/ | |
Software, algorithm | blastp | NIH NCBI | https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins | |
Software, algorithm | Clustal Omega | McWilliam et al., 2013 | https://www.ebi.ac.uk/Tools/msa/clustalo/ | |
Software, algorithm | Simply Phylogeny | Madeira et al., 2019 | https://www.ebi.ac.uk/Tools/phylogeny/simple_phylogeny/ | |
Software, algorithm | Geneious 9.14 | Biomatters Ltd | https://www.geneious.com/ | |
Software, algorithm | UCSF Chimera 1.13 | Pettersen et al., 2004 | https://www.cgl.ucsf.edu/chimera/ | |
Software, algorithm | Open Source PyMOL | Schroedinger LLC | https://github.com/schrodinger/pymol-open-source | |
Software, algorithm | I-TASSER | Roy et al., 2010 | https://zhanglab.ccmb.med.umich.edu/I-TASSER/ | |
Software, algorithm | IDT Codon Optimization Tool | Integrated DNA Technologies (IDT) | https://www.idtdna.com | |
Software, algorithm | MotionCor2 | Zheng et al., 2017 | https://omictools.com/motioncor2-tool | |
Software, algorithm | CTFFIND4 | Rohou and Grigorieff, 2015 | http://grigoriefflab.janelia.org/ctffind4 | |
Software, algorithm | SAMUEL | Liao Lab | https://liao.hms.harvard.edu/samuel | |
Software, algorithm | Sam Viewer | Liao Lab | https://liao.hms.harvard.edu/samviewer | |
Software, algorithm | Relion 3.0 | Scheres, 2012 | https://www3.mrc-lmb.cam.ac.uk/relion/index.php?title=Main_Page | |
Software, algorithm | SPIDER | Frank et al., 1996 | https://spider.wadsworth.org/spider_doc/spider/docs/spider.html | |
Software, algorithm | ResMap | Swint-Kruse and Brown, 2005 | http://resmap.sourceforge.net/ | |
Software, algorithm | Coot 0.8.9.1 | Emsley et al., 2010 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ | |
Software, algorithm | Phenix 1.14 | Adams et al., 2010 | http://www.phenix-online.org/ | |
Software, algorithm | XDS | Kabsch, 2010 | http://xds.mpimf-heidelberg.mpg.de/ | |
Software, algorithm | ACRIMBOLDO_LITE | Sammito et al., 2015 | http://chango.ibmb.csic.es/arcimboldo_lite | |
Software, algorithm | Phaser | McCoy et al., 2007 | https://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software | |
Software, algorithm | SHELX | Thorn and Sheldrick, 2013 | http://shelx.uni-goettingen.de/ | |
Software, algorithm | CCP4 | Winn et al., 2011 | http://www.ccp4.ac.uk/ | |
Software, algorithm | REFMAC5 | Murshudov et al., 1997 | http://www.ccp4.ac.uk/html/refmac5.html | |
Software, algorithm | Fiji-ImageJ 1.52h | Schindelin et al., 2012 | https://fiji.sc/ | |
Software, algorithm | UCSFImage4 | omicX | https://omictools.com/ucsfimage-tool | |
Other | 200 Mesh Gold Grids | EMS | FCF-200-Au | |
Other | 400 Mesh Cu Holy Carbon Grids | EMS | Q410CR1.3 | |