3UT9 | pdb_00003ut9

Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L)

X-RAY DIFFRACTION

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.494	α = 90
b = 109.533	β = 90
c = 174.822	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		PIXEL	PSI PILATUS 6M			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.80	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	2.2	92.819	99.8	0.054	12.3	5.4	104105	104105

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	99		0.507	0.507	0.734	0.382	1.5	3.4	14936

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	42.55	104004	2083	99.76	0.2572	0.2565	0.25	0.2892	0.28	RANDOM	87.9913

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]
5.37			-4.73		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.411
r_dihedral_angle_4_deg	19.361
r_dihedral_angle_3_deg	18.952
r_dihedral_angle_1_deg	6.071
r_scangle_it	1.886
r_mcangle_it	1.416
r_angle_refined_deg	1.362
r_scbond_it	1.256
r_mcbond_it	0.795
r_symmetry_hbond_refined	0.338

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.411
r_dihedral_angle_4_deg	19.361
r_dihedral_angle_3_deg	18.952
r_dihedral_angle_1_deg	6.071
r_scangle_it	1.886
r_mcangle_it	1.416
r_angle_refined_deg	1.362
r_scbond_it	1.256
r_mcbond_it	0.795
r_symmetry_hbond_refined	0.338
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.29
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6068
Nucleic Acid Atoms	5939
Solvent Atoms	140
Heterogen Atoms	33

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.