6IPU

Human nucleosome core particle containing 145 bp of DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NZD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291.15	manganese chloride, potassium chloride, potassium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.56	α = 90
b = 109.71	β = 90
c = 183.48	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		2017-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.99	94.16	99.6	0.021	0.997	17.4	12.2		148453

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.1	97.9		0.652	0.526	1.3	11.6

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	2NZD	1.99	94.16	145312	3035	99.6	0.237	0.236	0.263	RANDOM	74.55

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]
1.76			-3.11		1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.301
r_dihedral_angle_4_deg	21.693
r_dihedral_angle_3_deg	16.771
r_long_range_B_other	10.008
r_long_range_B_refined	10.006
r_scangle_other	6.308
r_dihedral_angle_1_deg	5.191
r_mcangle_it	4.56
r_mcangle_other	4.56
r_scbond_it	4.022
r_scbond_other	4.022
r_mcbond_it	3.042
r_mcbond_other	3.041
r_angle_refined_deg	1.474
r_angle_other_deg	1.426
r_chiral_restr	0.2
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6117
Nucleic Acid Atoms	5939
Solvent Atoms	114
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing