8Q36 | pdb_00008q36

Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG 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
3.02	59.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.194	α = 90
b = 109.563	β = 90
c = 183.675	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	2.6	48.83	93.6	0.999	19.6	12.5		62688

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	2.6	2.74			0.567

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.604	48.828	62632	1262	93.594	0.214	0.2126	0.22	0.2619	0.26	3	95.165

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]
1.614			-5.844		4.229

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.291
r_dihedral_angle_4_deg	21.496
r_dihedral_angle_3_deg	19.94
r_lrange_it	17.955
r_lrange_other	17.955
r_scangle_it	14.741
r_scangle_other	14.74
r_scbond_it	9.86
r_scbond_other	9.86
r_mcangle_it	9.844
r_mcangle_other	9.844
r_mcbond_it	6.948
r_mcbond_other	6.942
r_dihedral_angle_1_deg	6.776
r_angle_refined_deg	1.62
r_angle_other_deg	1.484
r_symmetry_xyhbond_nbd_refined	0.46
r_symmetry_nbd_other	0.221
r_nbd_refined	0.219
r_nbd_other	0.217
r_nbtor_refined	0.211
r_symmetry_nbd_refined	0.199
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.084
r_xyhbond_nbd_other	0.084
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.069
r_metal_ion_refined	0.018
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6257
Nucleic Acid Atoms	5939
Solvent Atoms
Heterogen Atoms	1

Software

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