3LZ0

Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KX4	NCP146b (pdb code 1KX4)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	K cacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.37	α = 90
b = 109.66	β = 90
c = 175.75	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	90	PIXEL	PSI PILATUS 6M		2009-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.5	93.04	90.6	0.08	7.8	4.6	65509	65509

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	61.9		0.384	0.384	1.9	2.1	6362

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	NCP146b (pdb code 1KX4)	2.5	93.04	65180	1317	89.97	0.268	0.269	0.268	0.318	RANDOM	109.277

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]
7.93			-7.46		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.721
r_dihedral_angle_3_deg	20.849
r_dihedral_angle_4_deg	18.838
r_dihedral_angle_1_deg	5.835
r_scangle_it	1.634
r_angle_refined_deg	1.453
r_mcangle_it	1.139
r_scbond_it	0.901
r_mcbond_it	0.635
r_symmetry_hbond_refined	0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.721
r_dihedral_angle_3_deg	20.849
r_dihedral_angle_4_deg	18.838
r_dihedral_angle_1_deg	5.835
r_scangle_it	1.634
r_angle_refined_deg	1.453
r_mcangle_it	1.139
r_scbond_it	0.901
r_mcbond_it	0.635
r_symmetry_hbond_refined	0.37
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5959
Nucleic Acid Atoms	5939
Solvent Atoms
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASES	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 R01GM157729.