6LA8

349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LAB	6LAB, 4QLC
experimental model	PDB	4QLC	6LAB, 4QLC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291.15	Calcium chloride, potassium chloride, sodium acetate (cryo-25% MPD)

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.055	α = 90
b = 184.073	β = 90
c = 223.367	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	98.15	PIXEL	DECTRIS PILATUS 2M-F		2018-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.4	49.32	99.8	0.151	0.163	0.062	1	12.1	13.3		69141

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	3.59			0.41	1.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6LAB, 4QLC	3.4	49.32	67687	1381	99.74	0.2076	0.2064	0.2646	RANDOM	149.241

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-6.56			-3.33		9.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.409
r_dihedral_angle_3_deg	19.427
r_dihedral_angle_4_deg	16.609
r_dihedral_angle_1_deg	5.935
r_angle_other_deg	2.323
r_angle_refined_deg	1.262
r_chiral_restr	0.069
r_bond_other_d	0.027
r_gen_planes_other	0.007
r_bond_refined_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.409
r_dihedral_angle_3_deg	19.427
r_dihedral_angle_4_deg	16.609
r_dihedral_angle_1_deg	5.935
r_angle_other_deg	2.323
r_angle_refined_deg	1.262
r_chiral_restr	0.069
r_bond_other_d	0.027
r_gen_planes_other	0.007
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12717
Nucleic Acid Atoms	14311
Solvent Atoms
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.