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Open data
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Basic information
Entry | Database: PDB / ID: 7d8c | ||||||
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Title | Crystal structure of the Cas12i1-crRNA binary complex | ||||||
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![]() | RNA BINDING PROTEIN / The RNP Complex 3 | ||||||
Function / homology | CITRIC ACID / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, B. / Luo, D.Y. / Li, Y. / OuYang, S.Y. | ||||||
![]() | ![]() Title: Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1. Authors: Zhang, B. / Luo, D. / Li, Y. / Perculija, V. / Chen, J. / Lin, J. / Ye, Y. / Ouyang, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249.6 KB | Display | ![]() |
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PDB format | ![]() | 196.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7d2lSC ![]() 7d3jC ![]() 7eu9C 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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Unit cell |
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Components
#1: Protein | Mass: 128216.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: RNA chain | Mass: 14086.325 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
#3: RNA chain | Mass: 919.620 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
#4: Chemical | ChemComp-CIT / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.01 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium citrate (pH 5.2), 17% (w/v) Polyethylene glycol 3350, 2% Tacsimate (pH 4.0), 0.15 M sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→57.42 Å / Num. obs: 25821 / % possible obs: 99.9 % / Redundancy: 38.6 % / CC1/2: 0.998 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 3.6→3.85 Å / Num. unique obs: 4599 / CC1/2: 0.955 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7D2L Resolution: 3.6→57.42 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.88 / SU B: 55.123 / SU ML: 0.793 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.702 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 200 Å2 / Biso mean: 144.549 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 3.6→57.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.6→3.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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