6LAB | pdb_00006lab

169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0

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	4.5	291.15	Calcium chloride, potassium chloride, sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.799	α = 90
b = 102.76	β = 97.4
c = 218.05	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		2015-09-18	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)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.2	216.23	99.3	0.108	0.151	0.105	0.993	5.3	3		75580

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.37	96.6		0.811	0.557	1.2	2.8

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	3.2	39.892	75562	1469	99.242	0.202	0.201	0.21	0.2619	0.26	RANDOM	115.807

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]
-4.512		4.868	-3.039		6.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.27
r_dihedral_angle_3_deg	19.03
r_dihedral_angle_4_deg	17.077
r_lrange_it	16.931
r_lrange_other	16.931
r_scangle_it	13.096
r_scangle_other	13.095
r_mcangle_it	10.924
r_mcangle_other	10.924
r_scbond_it	8.316
r_scbond_other	8.316
r_mcbond_it	7.1
r_mcbond_other	7.098
r_dihedral_angle_1_deg	6.833
r_angle_other_deg	1.392
r_angle_refined_deg	1.289
r_symmetry_xyhbond_nbd_refined	0.369
r_nbd_other	0.334
r_symmetry_nbd_refined	0.314
r_nbtor_refined	0.207
r_symmetry_nbd_other	0.206
r_nbd_refined	0.19
r_metal_ion_refined	0.162
r_xyhbond_nbd_refined	0.148
r_xyhbond_nbd_other	0.128
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13379
Nucleic Acid Atoms	13846
Solvent Atoms
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing