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Title:3D Cryo-negative EM structure of nucleosome-bound SWR1
Authors:Nguyen VQ, Ranjan A, Stengel F, Wei D, Aebersold R, Wu C, Leschziner AE
Sample:SWR1 (S.c.) bound to recombinant nucleosomes
Method:Single particle reconstruction (34 angstroms resolution)
Related entries in frame:EMD-5626
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Sample
Sample name: SWR1 (S.c.) bound to recombinant nucleosomes
Theoretical molecular weight of the sample: 1.2
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details
1proteinSWR1falseSaccharomyces cerevisiae
Experiment
Specimen state: Particle
Specimen preparation:
pHSpecimen conc.DetailsStainingSpecimen support details
7.4 mg/mL25 mM HEPES-KOH, pH 7.6, 1 mM EDTA, 2 mM MgCl2, 0.01% NP-40, 1 mM DTT, 100 mM KClCryo-negative staining with 2% uranyl formate followed by freezing in liquid nitrogen200 mesh Quantifoil with glow-discharged thin carbon support
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
NITROGEN% KNONECryo-negative stain with 2% uranyl formate. Blotted and frozen in liquid nitrogen. ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI TECNAI F20120 kVFLOOD BEAMBRIGHT FIELD2.0 mm500 nm2000 nm6200086700FIELD EMISSION GUNGATAN US4000 4Kx4K mm

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
GATAN LIQUID NITROGEN°° eV100 K K K mrad20 e/Å2Low-dose imaging20-MAY-2012
Processing
Protocol:Projection matching
Software:RELION
CTF correction:EMAN2
Number of particles:12000
Imposed symmetry:C1
Resolution by author:34 Å
Resolution method:RELION gold-standard
Processing details:The dataset was classified using the maximum-likelihood based method in the RELION program. A selected 3D class was then refined against particles assigned to the class using RELION's "Autorefine" function.
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
30015 μm/pixel
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails