8Q3X

Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IPU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.105	α = 90
b = 109.609	β = 90
c = 183.767	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	PIXEL	DECTRIS PILATUS 2M-F		2018-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.04	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.3	48.93	99.9	1	27.3	12.2		97275

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	2.3	2.43			0.651

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.301	48.93	97189	1952	99.832	0.224	0.2235	0.2623	3	94.074

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]
4.758			-4.784		0.026

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.82
r_dihedral_angle_4_deg	21.142
r_dihedral_angle_3_deg	18.892
r_lrange_it	15.477
r_lrange_other	15.477
r_scangle_it	12.244
r_scangle_other	12.243
r_mcangle_other	8.629
r_mcangle_it	8.628
r_scbond_it	8.289
r_scbond_other	8.288
r_dihedral_angle_1_deg	6.272
r_mcbond_it	6.176
r_mcbond_other	6.173
r_angle_other_deg	2.441
r_angle_refined_deg	1.474
r_symmetry_nbd_other	0.242
r_symmetry_xyhbond_nbd_refined	0.21
r_nbtor_refined	0.207
r_nbd_refined	0.205
r_nbd_other	0.198
r_symmetry_nbd_refined	0.155
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.076
r_bond_other_d	0.028
r_gen_planes_other	0.013
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6215
Nucleic Acid Atoms	5939
Solvent Atoms
Heterogen Atoms	24

Software

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