SASDCT6: 12N12 nucleosome in 60% sucrose with ADP-BeF3 (169 bp DNA (145 bp...

Basic information

Entry

Database: SASBDB / ID: SASDCT6

Sample

12N12 nucleosome in 60% sucrose with ADP-BeF3

• 169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) (DNA), DNA
• Histone H2A type 1 (protein), H2A, Xenopus laevis
• Histone H2B 1.1 (protein), H2B, Xenopus laevis
• Histone H3.2 (protein), H3, Xenopus laevis
• Histone H4 (protein), H4, Xenopus laevis

• Biological species: Xenopus laevis (African clawed frog)

Models

Sample

• Sample: Name: 12N12 nucleosome in 60% sucrose with ADP-BeF3 / Specimen concentration: 1.1 mg/ml / Entity id: 769 / 770 / 771 / 772 / 773
• Buffer: Name: 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, ADP-BeF3 (0.5 mM ADP, 4 mM NaF, 0.6 mM BeCl2); pH: 7.8 / Comment: 60% sucrose ADP-BeF3

Entity #769

Name: DNA / Type: DNA
Description: 169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)
Formula weight: 52.468 / Num. of mol.: 1
Sequence:

CTTTCAGCTG ATATCGATGT ATATATCTGA CACGTGCCTG GAGACTAGGG AGTAATCCCC TTGGCGGTTA AAACGCGGGG GACAGCGCGT ACGTGCGTTT AAGCGGTGCT AGAGCTGTCT ACGACCAATT GAGCGGCCTC GGCACCGGGA TCTTGATATC AGCTGAAAG

Entity #770

Name: H2A / Type: protein / Description: Histone H2A type 1 / Formula weight: 13.966 / Num. of mol.: 1 / Source: Xenopus laevis
Sequence:

MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVRN DEELNKLLGG VTIAQGGVLP NIQSVLLPKK TESAKSAKSK

Entity #771

Name: H2B / Type: protein / Description: Histone H2B 1.1 / Formula weight: 13.934 / Num. of mol.: 1 / Source: Xenopus laevis
Sequence:

MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

Entity #772

Name: H3 / Type: protein / Description: Histone H3.2 / Formula weight: 15.388 / Num. of mol.: 1 / Source: Xenopus laevis
Sequence:

MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

Entity #773

Name: H4 / Type: protein / Description: Histone H4 / Formula weight: 11.367 / Num. of mol.: 1 / Source: Xenopus laevis
Sequence:

MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

Experimental information

• Beam: Instrument name: Cornell High Energy Synchrotron Source (CHESS) G1; City: Ithaca, NY / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1109 Å / Dist. spec. to detc.: 2.08 mm
• Detector: Name: Pilatus 200K / Type: Pilatus / Pixsize x: 172 mm

Scan

Title: 12N12 nucleosome in 60% sucrose with ADP-BeF3 / Measurement date: Oct 24, 2015 / Storage temperature: 25 °C / Cell temperature: 25 °C / Exposure time: 10 sec. / Number of frames: 40 / Unit: 1/A /

	Min	Max
Q	0.016	0.26

Result

Experimental MW: 105 kDa / Type of curve: single_conc
Comments: 12N12 nucleosome measured in 60% sucrose and ADP-BeF3. Due to contrast matching between the solvent and histone proteins (due to sucrose), the measured signal is dominated by the DNA component. The model was generated using 3D-DART and custom scripts written in Pymol. The percentage-weighting of each model in the ensemble ('XXXperc') is noted in the model key below: SASDCT6_fit1_model1 = 12N12_ADP_01_100perc

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.0222	0.00013	0.021622	0.000176
Radius of gyration, Rg	4.937 nm	0.026	4.812 nm	0.52

	Min	Max
D	-	14
Guinier point	1	12