REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Chemicals, Peptides, and Recombinant Proteins | ||
HEPES | Sigma-Aldrich | H3375-250G |
Sodium citrate tribasic dihydrate | Sigma-Aldrich | C8532-1KG |
Citric acid | Sigma-Aldrich | C0759-500G |
Sodium acetate | Sigma-Aldrich | S7545-1KG |
Magnesium chloride hexahydrate | Sigma-Aldrich | M2393-500G |
Potassium sulfate | Sigma-Aldrich | P9458-250G |
Lithium chloride | Sigma-Aldrich | L9650-500G |
glycerol | Sigma-Aldrich | G5516-1L |
DL-Dithiothreitol (DTT) | Sigma-Aldrich | D9163-25G |
Pentaerythritol propoxylate (5/4 PO/OH) | Sigma-Aldrich | 41-8749-500ML |
PEG 600 | Sigma-Aldrich | 202401-500G |
PEG 3,350 | Sigma-Aldrich | 88276-1KG-F |
PEG 6,000 | Sigma-Aldrich | 81255-1KG |
T7 RNA polymerase | Home-made | N/A |
Ulp1 | Home-made | N/A |
Toluidine Blue | AMRESCO | 0672-25G |
Urea | AMRESCO | 0378-5KG |
Spermidine | Sigma-Aldrich | S2626-1G |
ATP | Sigma-Aldrich | A2383 |
UTP | Sigma-Aldrich | U6625 |
CTP | Sigma-Aldrich | C1506 |
GTP | Sigma-Aldrich | G8877 |
AxyPrep Plasmid Maxiprep Kit 25-prep | Axygen | AP-MX-P-25G |
Critical Commercial Assays | ||
Chelating Sepharose Fast Flow | GE Healthcare | Cat# 17-0575-02 |
HiTrap Heparin HP | GE Healthcare | Cat# 17-0407-03 |
HiTrap SP HP | GE Healthcare | Cat# 17-1152-01 |
Superdex 200 Increase, 10/300 GL | GE Healthcare | Cat# 28-9909-44 |
Deposited Data | ||
The coordinates of Nme1Cas9-sgRNA complex | This paper | PDB: 6JDQ |
The coordinates of Nme1Cas9 (His588Ala)-sgRNA-DNA in catalytic state | This paper | PDB: 6JDV |
The coordinates of Nme1Cas9-sgRNA-DNA in seed-base paring state | This paper | PDB: 6KC7 |
The coordinates of Nme1Cas9(WT)-sgRNA-DNA in post-cleavage state | This paper | PDB: 6KC8 |
The coordinates of Nme2Cas9-sgRNA-dsDNA-0nt complex | This paper | PDB: 6JFU |
The coordinates of Nme2Cas9-sgRNA-dsDNA-5nt complex | This paper | PDB: 6JE3 |
The coordinates of Nme1Cas9-sgRNA-AcrIIC3 complex | This paper | PDB: 6JE9 |
The coordinates of Nme1Cas9-sgRNA-AcrIIC3-dsDNA complex | This paper | PDB: 6JE4 |
The coordinates of SpyCas9-sgRNA-DNA complex | Anders et al., 2014. | PDB: 4UN3 |
The coordinates of SauCas9-sgRNA-DNA complex | Nishimasu et al., 2015. | PDB: 5CZZ |
The coordinates of SpyCas9-sgRNA-DNA complex | Jiang et al., 2016. | PDB: 5F9R |
Experimental Models: Organisms/Strains | ||
Escherichia coli Rosetta (DE3) | Novagen | Cat# 70954-3 |
Recombinant DNA | ||
pET28a-Nme1Cas9, various mutants | This paper | N/A |
pET28a-Nme2Cas9, various mutants | This paper | N/A |
pET28a-AcrIIC3 | This paper | N/A |
pET30b-Nme1Cas9 | This paper | N/A |
Oligonucleotides | ||
147-nt SgRNA sequence. GGUCACUCUGCU AUUUAACUUUACGUUGUAGCUCCCUUUC UCAUUUCGGAAACGAAAUGAGAACCGUUG CUACAAUAAGGCCGUCUGAAAAGAUGUGC CGCAACGCUCUGCCCCUUAAAGCUCCUGC UUUAAGGGGCAUCGUUUAUC |
This paper | N/A |
135-nt SgRNA sequence. GGUCACUCUGCUAU UUAACUUUACGUUGUAGCUCCCUUUCUCG AAAGAGAACCGUUGCUACAAUAAGGCCGUC UGAAAAGAUGUGCCGCAACGCUCUGCCCC UUAAAGCUCCUGCUUUAAGGGGCAUCGU UUAUC |
This paper | N/A |
122-nt SgRNA sequence. GGUCACUCUUCUAU UUACCUAUACGUUGUAGCUCCCUUUCUCAUU UCGGAAACGAAAUGAGAACCGUUGCUACAAUA AGGCCGUCUGAAAAGAUGUGCCGCAACGCUC UUUCUAGAGCGUUC |
This paper | N/A |
102-nt SgRNA sequence. GGACUCACGACGCA UUACCUUUACGUUGUAGCUCCCUUUCUCAUU UCGGAAACGAAAUGAGAACCGUUGCUACAAUA AGGCCGUCUGAAAAGAUGUGCCAUC |
This paper | N/A |
SpyCas9 sgRNA sequence. GGAAAUUAGGUGCGC UUGGCGUUUUAGAGCUAGAAAUAGCAAGUUAAAA UAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUC |
This paper | N/A |
SauCas9 sgRNA sequence. GGUCUGCUAUUUCUA UUUACGUUUUAGUACUCUGGAAACAGAAUCUAC UAAAACAAGGCAAAAUGCCGUGUUUAUC UCGUCAACUUGUUGGCGAGAUC |
This paper | N/A |
DNA sequences | This paper | Table S4 |
Plasmids and primers | This paper | Table S5 |
Software and Algorithms | ||
PHENIX | Adams et al., 2002 | http://www.phenix-online.org/ |
HKL2000 | Otwinowski and Minor, 1997 | http://www.hkl-xray.com/ |
COOT | Emsley et al., 2010 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
PyMOL | Molecular Graphics System, Version 1.8 Schrödinger, LLC | https://www.pymol.org/2/ |
PHASER | McCoy et al., 2007 | https://www-structmed.cimr.cam.ac.uk/phaser_obsolete/ |
Other | ||
Amicon Ultra Centrifugal Filters Ultracel-50K | Merck Millipore Ltd | UFC903096 |
Amicon Ultra Centrifugal Filters Ultracel-10K | Merck Millipore Ltd | UFC801096 |
3 Well Midi Crystallization Plate (Swissci) | HAMPTON RESEARCH | Cat# HR3-125 |