5XF3

Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MNN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.19	α = 90
b = 109.4	β = 90
c = 174.82	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	100	CCD	PSI PILATUS 6M		2014-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.5	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.6	58.27	99.9	15	5.8		64455

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	99.6		0.505		5.4

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	3MNN	2.6	52.748	63050	1303	99.8	0.23534	0.23458	0.27017	RANDOM	105.554

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]
9.65			-7.35		-2.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.454
r_dihedral_angle_4_deg	20.623
r_dihedral_angle_3_deg	17.142
r_long_range_B_refined	16.016
r_long_range_B_other	16.015
r_scangle_other	11.892
r_mcangle_it	8.156
r_mcangle_other	8.155
r_scbond_it	7.899
r_scbond_other	7.895
r_dihedral_angle_1_deg	5.761
r_mcbond_it	5.707
r_mcbond_other	5.699
r_angle_refined_deg	1.452
r_angle_other_deg	1.292
r_chiral_restr	0.081
r_bond_refined_d	0.009
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	6094
Nucleic Acid Atoms	5939
Solvent Atoms
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement