7XVL | pdb_00007xvl

Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UT9	3UT9, 4QLC
experimental model	PDB	4QLC	3UT9, 4QLC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 213.85	α = 90
b = 102.46	β = 100.49
c = 218.289	γ = 90

Symmetry
Space Group	P 1 21 1

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		2017-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1	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	3.506	88.439	100	1	8	6.1		117231

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	3.51	3.57	100		0.37	1.1	5.9

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 (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	THROUGHOUT	3UT9, 4QLC	3.506	88.439	112443	2266	95.918	0.208	0.2062	0.21	0.2795	0.28	RANDOM	147.315

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]
0.062		0.533	-2.352		1.958

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.571
r_lrange_it	24.996
r_lrange_other	24.996
r_scangle_it	19.237
r_scangle_other	19.237
r_dihedral_angle_3_deg	19.075
r_dihedral_angle_4_deg	18.325
r_mcangle_other	14.433
r_mcangle_it	14.432
r_scbond_it	12.143
r_scbond_other	12.142
r_mcbond_it	9.497
r_mcbond_other	9.492
r_dihedral_angle_1_deg	6.985
r_angle_other_deg	1.436
r_angle_refined_deg	1.349
r_nbd_other	0.437
r_symmetry_xyhbond_nbd_refined	0.385
r_symmetry_nbd_refined	0.334
r_symmetry_nbd_other	0.216
r_nbtor_refined	0.211
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.16
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.071
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24850
Nucleic Acid Atoms	27724
Solvent Atoms
Heterogen Atoms

Software

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