6W4L

The crystal structure of a single chain H2B-H2A histone chimera from Xenopus laevis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.9	291	0.2M sodium thiocyanate, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.09	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.793	α = 90
b = 44.679	β = 117.27
c = 66.45	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2017-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

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	1.31	26.71	99.4	0.058	0.069	0.036	0.999	5.6	3.7		38073			13.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.31	1.39	99.8		0.892	1.052	0.55	0.619		3.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1KX5	1.31	20	36283	1776	99.28	0.1712	0.1695	0.2063	RANDOM	20.418

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]
0.47		-0.01	-0.96		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.634
r_dihedral_angle_4_deg	19.937
r_sphericity_free	14.972
r_dihedral_angle_3_deg	13.83
r_sphericity_bonded	5.968
r_dihedral_angle_1_deg	4.5
r_rigid_bond_restr	1.788
r_angle_refined_deg	1.541
r_angle_other_deg	1.057
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.634
r_dihedral_angle_4_deg	19.937
r_sphericity_free	14.972
r_dihedral_angle_3_deg	13.83
r_sphericity_bonded	5.968
r_dihedral_angle_1_deg	4.5
r_rigid_bond_restr	1.788
r_angle_refined_deg	1.541
r_angle_other_deg	1.057
r_chiral_restr	0.101
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1375
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	9

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing
Coot	model building

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 R01GM133198.