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- PDB-5w1i: Crystal structure of LbaCas13a (C2c2) bound to mature crRNA (20-n... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w1i | ||||||
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Title | Crystal structure of LbaCas13a (C2c2) bound to mature crRNA (20-nt spacer) | ||||||
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![]() | RNA BINDING PROTEIN/RNA / Nuclease RNA binding protein / ![]() | ||||||
Function / homology | IODIDE ION / ![]() ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Knott, G.J. / Doudna, J.A. | ||||||
![]() | ![]() Title: Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme. Authors: Knott, G.J. / East-Seletsky, A. / Cofsky, J.C. / Holton, J.M. / Charles, E. / O'Connell, M.R. / Doudna, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 615.2 KB | Display | ![]() |
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PDB format | ![]() | 489 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5w1hSC ![]() 5wlhC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: RNA chain | Mass: 16889.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Protein | Mass: 169192.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-IOD / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.53 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M ammonium iodide, 20 - 25 % PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→48.57 Å / Num. obs: 161267 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.466 / % possible all: 96.6 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5W1H Resolution: 2.2→48.42 Å / SU ML: 0.295 / Cross valid method: FREE R-VALUE / σ(F): 1.959 / Phase error: 25.872
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→48.42 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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