Bacterial and Virus Strains |
|
E. coli BL21(DE3) |
Novagen |
69450 |
|
Chemicals, Peptides, and Recombinant Proteins |
|
Recombinant DNaseI (RNase free) |
Roche |
03539121103 |
T4 PNK |
ThermoFisher |
EK0031 |
Graphene Oxide |
Sigma-Aldrich |
763705-25ML |
IPTG |
ThermoFisher |
R0392 |
|
Critical Commercial Assays |
|
NEBNext Ultra II DNA Library Prep Kit for Illumina |
NEB |
E7645S |
|
Deposited Data |
|
Cas1Cas2Csn2 single complex bound to DNA |
This work |
PDB: 6QXF, EMD: 4668 |
Cas1Cas2Csn2 dimer complex bound to DNA |
This work |
PDB: 6QXT, EMD: 4670 |
Cas1Cas2Csn2 filament complex bound to DNA |
This work |
PDB: 6QY3, EMD: 4671 |
|
Oligonucleotides |
|
acgaggagctattggcacaacttaca (prospacer duplex forward) |
Macrogen |
N/A |
agttgtgccaatagctcctcgtcatt (prospacer duplex reverse) |
Metabion |
N/A |
agatatcctacgaggttttagagctgtgttgtttcgaatggttccaaaacaaattctaaacgctaaagaggaag (CRISPR3 Leader-Repeat-Spacer duplex for in vitro integration reaction forward) |
Metabion |
N/A |
cttcctctttagcgtttagaatttgttttggaaccattcgaaacaacacagctctaaaacctcgtaggatatct (CRISPR3 Leader-Repeat-Spacer duplex for in vitro integration reaction forward reverse) |
Metabion |
N/A |
|
Recombinant DNA |
|
pCRISPR3 (expressing full S. thermophilus CRISPR3 loci) |
Sapranauskas et al., 2011 |
N/A |
pCas9- (Cas9 deletion, containing the rest of the CRISPR3 loci) |
Sapranauskas et al., 2011 |
N/A |
pCas2- (Cas2 deletion, containing the rest of the CRISPR3 loci) |
Sapranauskas et al., 2011 |
N/A |
pCsn2- (Csn2 deletion, containing the rest of the CRISPR3 loci) |
Sapranauskas et al., 2011 |
N/A |
pCas1Strep (expressing C-Term Strep-tagged Cas1) |
This work |
N/A |
pCR3ΔCRISPR (CRISPR region deletion, containing the rest of CRISPR3 loci) |
This work |
N/A |
pCR3Δtracr (tracrRNA deletion, contain the rest of CRISPR3 locus) |
Karvelis et al., 2013 |
N/A |
|
Software and Algorithms |
|
Phyre2 webserver |
Kelley et al., 2015 |
http://www.sbg.bio.ic.ac.uk/∼phyre2/html/page.cgi?id=index |
Chimera |
Goddard et al., 2007 |
https://www.cgl.ucsf.edu/chimera/ |
COOT |
Emsley et al., 2010 |
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
Refmac jelly-body refinement script |
Murshudov et al., 1997 |
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/em_fitting/em_fitting.html |
PHENIX real space refine |
Afonine et al., 2018 |
https://www.phenix-online.org/documentation/reference/real_space_refine.html |
Motioncorr |
Li et al., 2013 |
https://cryoem.ucsf.edu/software/driftcorr.html |
Motioncor2 |
Zheng et al., 2017 |
https://msg.ucsf.edu/em/software/motioncor2.html |
Gctf |
Zhang, 2016 |
https://www.mrc-lmb.cam.ac.uk/kzhang/ |
Gautomatch |
N/A |
https://www.mrc-lmb.cam.ac.uk/kzhang/ |
IMAGIC |
van Heel and Keegstra, 1981 |
https://download.imagescience.de/index.html |
RELION3 |
Zivanov et al., 2018 |
https://www3.mrc-lmb.cam.ac.uk/relion/index.php?title=Main_Page |
cryoSPARC |
Punjani et al., 2017 |
https://guide.cryosparc.com/install.html |
GraphPad Prism 8 |
N/A |
https://www.graphpad.com/scientific-software/prism/ |