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- PDB-5xwp: Crystal structure of LbuCas13a-crRNA-target RNA ternary complex -

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Basic information

Entry
Database: PDB / ID: 5xwp
TitleCrystal structure of LbuCas13a-crRNA-target RNA ternary complex
DescriptorUncharacterized protein/RNA Complex
KeywordsRNA BINDING PROTEIN/RNA / LbuCas13a / C2c2 / crRNA / target RNA / RNA BINDING PROTEIN-RNA complex
Specimen sourceLeptotrichia buccalis / bacteria / レプトトリキア・ブカリス
Synthetic construct
MethodX-ray diffraction (3.086 Å resolution / SAD)
AuthorsLiu, L. / Li, X. / Li, Z. / Wang, Y.
CitationCell, 2017, 170, 714-726.e10

Cell, 2017, 170, 714-726.e10 StrPapers
The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a.
Liu, L. / Li, X. / Ma, J. / Li, Z. / You, L. / Wang, J. / Wang, M. / Zhang, X. / Wang, Y.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 30, 2017 / Release: Sep 13, 2017

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Assembly

Deposited unit
A: Uncharacterized protein
C: RNA (59-MER)
D: RNA (30-MER)
E: RNA (59-MER)
F: RNA (30-MER)
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)336,3546
Polyers336,3546
Non-polymers00
Water21612
#1
A: Uncharacterized protein
C: RNA (59-MER)
D: RNA (30-MER)


Theoretical massNumber of molelcules
Total (without water)168,1773
Polyers168,1773
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)17080
ΔGint (kcal/M)-124
Surface area (Å2)61120
MethodPISA
#2
E: RNA (59-MER)
F: RNA (30-MER)
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)168,1773
Polyers168,1773
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)16210
ΔGint (kcal/M)-127
Surface area (Å2)61480
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)95.576, 132.870, 139.960
Angle α, β, γ (deg.)90.00, 90.80, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Polypeptide(L)Uncharacterized protein


Mass: 139627.047 Da / Num. of mol.: 2 / Mutation: R1048A, H1053A
Source: (gene. exp.) Leptotrichia buccalis / bacteria / レプトトリキア・ブカリス
References: UniProt: C7NBY4
#2: RNA chainRNA (59-MER)


Mass: 18869.348 Da / Num. of mol.: 2 / Source: (synth.) Synthetic construct
#3: RNA chainRNA (30-MER)


Mass: 9680.769 Da / Num. of mol.: 2 / Source: (synth.) Synthetic construct
#4: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 / Density percent sol: 54.51
Crystal growTemp: 289 K / Method: VAPOR DIFFUSION, HANGING DROP / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 0.1 M L-Proline, 8% PEG 3350

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SSRF BEAMLINE BL17U1 / Synchrotron site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785
DetectorType: RAYONIX MX-225 / Detector: CCD / Collection date: Mar 21, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionD resolution high: 3.08 Å / D resolution low: 5 Å / Number obs: 61255 / Rmerge I obs: 0.185 / NetI over sigmaI: 14 / Redundancy: 15 / Percent possible obs: 98.6
Reflection shellRmerge I obs: 0.558 / Highest resolution: 3.08 Å / Lowest resolution: 3.13 Å / MeanI over sigI obs: 3.5 / Redundancy: 1 / Percent possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefineMethod to determine structure: SAD / Overall SU ML: 0.44 / Cross valid method: FREE R-VALUE / Sigma F: 1.52 / Overall phase error: 22.72 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.2437 / R factor R work: 0.2185 / R factor obs: 0.2197 / Highest resolution: 3.086 Å / Lowest resolution: 48.179 Å / Number reflection R free: 2881 / Number reflection obs: 61255 / Percent reflection R free: 4.7 / Percent reflection obs: 95.1
Refine hist #LASTHighest resolution: 3.086 Å / Lowest resolution: 48.179 Å
Number of atoms included #LASTProtein: 18100 / Nucleic acid: 3726 / Ligand: 0 / Solvent: 12 / Total: 21838
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01322568
X-RAY DIFFRACTIONf_angle_d1.59431192
X-RAY DIFFRACTIONf_dihedral_angle_d24.7539042
X-RAY DIFFRACTIONf_chiral_restr0.1043580
X-RAY DIFFRACTIONf_plane_restr0.0073343
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.08590.35710.30943.1365114210773.00
3.13650.33340.30463.1906123240683.00
3.19060.32230.30503.2486148250487.00
3.24860.35460.29263.3111125265591.00
3.31110.31490.27943.3786127272994.00
3.37860.30320.28283.4521115276494.00
3.45210.30660.27623.5323155276896.00
3.53230.27880.25683.6207163279196.00
3.62070.30710.23983.7185138281297.00
3.71850.22840.22463.8279119285697.00
3.82790.22600.22053.9514170279597.00
3.95140.21730.20474.0925139286398.00
4.09250.23780.19814.2563150284098.00
4.25630.22290.18404.4499112290198.00
4.44990.18670.18434.6843162289499.00
4.68430.20050.17524.9775129291799.00
4.97750.21810.18335.36141542915100.00
5.36140.22150.19995.90011202926100.00
5.90010.22340.20876.75181512950100.00
6.75180.21160.19368.49901322957100.00
8.49900.20070.191348.18481353024100.00

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