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- PDB-5vvj: Cas1-Cas2 bound to half-site intermediate -

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Basic information

Entry
Database: PDB / ID: 5vvj
TitleCas1-Cas2 bound to half-site intermediate
DescriptorCRISPR-associated endonuclease Cas1
CRISPR-associated endoribonuclease Cas2/DNA Complex
KeywordsHYDROLASE/DNA / Complex / DNA / HYDROLASE-DNA complex
Specimen sourceEscherichia coli (strain k12) / bacteria /
Synthetic construct
MethodX-ray diffraction (3.89 Å resolution / Molecular replacement)
AuthorsWright, A.V. / Knott, G.J. / Doxzen, K.W. / Doudna, J.A.
CitationScience, 2017, 357, 1113-1118

Science, 2017, 357, 1113-1118 Yorodumi Papers
Structures of the CRISPR genome integration complex.
Wright, A.V. / Liu, J.J. / Knott, G.J. / Doxzen, K.W. / Nogales, E. / Doudna, J.A.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 19, 2017 / Release: Aug 2, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Sep 27, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2
F: CRISPR-associated endoribonuclease Cas2
G: DNA (28-MER)
H: DNA (112-MER)


Theoretical massNumber of molelcules
Total (without water)197,3298
Polyers197,3298
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)27870
ΔGint (kcal/M)-172
Surface area (Å2)65460
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)75.067, 183.113, 196.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Polypeptide(L)
CRISPR-associated endonuclease Cas1


Mass: 33235.418 Da / Num. of mol.: 4
Source: (gene. exp.) Escherichia coli (strain k12) / bacteria /
References: UniProt: Q46896, EC: 3.1.-.-
#2: Polypeptide(L)CRISPR-associated endoribonuclease Cas2


Mass: 10584.264 Da / Num. of mol.: 2
Source: (gene. exp.) Escherichia coli (strain k12) / bacteria /
References: UniProt: P45956, EC: 3.1.-.-
#3: DNA chainDNA (28-MER)


Mass: 8680.646 Da / Num. of mol.: 1 / Source: (synth.) Synthetic construct
#4: DNA chainDNA (112-MER)


Mass: 34538.016 Da / Num. of mol.: 1 / Source: (synth.) Synthetic construct

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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: 3.43 / Density percent sol: 64.13
Crystal growTemp: 281 K / Method: VAPOR DIFFUSION, HANGING DROP / pH: 6.5
Details: 100 mM MES, pH 6.5, 10% (w/v) poly(ethylene glycol) (PEG) monomethyl ether (MME) 5000, 12% (v/v) propanol

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Data collection

DiffractionMean temperature: 80 kelvins
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 8.3.1 / Synchrotron site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Collection date: Apr 20, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 126.51 Å2 / D resolution high: 3.28 Å / D resolution low: 196.92 Å / Number obs: 40983 / CC half: 0.998 / Rmerge I obs: 0.668 / Rpim I all: 0.195 / Rrim I all: 0.697 / NetI over sigmaI: 3.3 / Redundancy: 12.3 / Percent possible obs: 96.1
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionCC halfRpim I allRrim I allRedundancyPercent possible all
10.3163.2803.4100.0574.94011.5653.90066.400
0.06411.820196.9200.9990.0220.0689.700100.000

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Phasing

PhasingMethod: MR

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Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DS5
Overall SU ML: 0.7 / Cross valid method: FREE R-VALUE / Sigma F: 1.34 / Overall phase error: 38.09
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 549.16 Å2 / B iso mean: 158.4474 Å2 / B iso min: 52.96 Å2
Least-squares processR factor R free: 0.329 / R factor R work: 0.2882 / R factor obs: 0.2903 / Highest resolution: 3.89 Å / Lowest resolution: 134.096 Å / Number reflection R free: 1326 / Number reflection obs: 25669 / Percent reflection R free: 5.17 / Percent reflection obs: 99.79
Refine hist #finalHighest resolution: 3.89 Å / Lowest resolution: 134.096 Å / Number residues total: 1352
Number of atoms included #finalProtein: 9534 / Nucleic acid: 2353 / Ligand: 0 / Solvent: 0 / Total: 11887
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312347
X-RAY DIFFRACTIONf_angle_d0.54017228
X-RAY DIFFRACTIONf_chiral_restr0.0381983
X-RAY DIFFRACTIONf_plane_restr0.0041803
X-RAY DIFFRACTIONf_dihedral_angle_d18.0076981
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 9 / Percent reflection obs: 1

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection all
3.89000.45910.38964.045813326592792
4.04580.34770.35564.229911526832798
4.22990.37140.32024.452913526742809
4.45290.33680.29844.732014026842824
4.73200.32350.29535.097315826382796
5.09730.36990.30345.610315526822837
5.61030.37060.30176.422116727022869
6.42210.29690.28208.091016227312893
8.09100.28490.2397134.175816128903051

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