4LXL

Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxylic acid and H3K9me3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	24% PEG8000, 0.2M magnesium acetate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.364	α = 90
b = 78.475	β = 90
c = 83.893	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	100	CCD	ADSC QUANTUM 4r		2013-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2	1	SPring-8	BL12B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.87	30	99.4	0.043		12.5	30463	30173	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.87	1.94	98		0.368		11.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2YBS	1.87	28.67	30173	28644	1529		0.1789	0.1765	0.2224	RANDOM	26.5967

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]
0.52			-1.47		0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.029
r_dihedral_angle_3_deg	18.352
r_dihedral_angle_4_deg	18.093
r_dihedral_angle_1_deg	7.22
r_scbond_it	5.12
r_mcangle_it	4.723
r_mcbond_it	3.603
r_angle_refined_deg	1.375
r_chiral_restr	0.123
r_gen_planes_refined	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.029
r_dihedral_angle_3_deg	18.352
r_dihedral_angle_4_deg	18.093
r_dihedral_angle_1_deg	7.22
r_scbond_it	5.12
r_mcangle_it	4.723
r_mcbond_it	3.603
r_angle_refined_deg	1.375
r_chiral_restr	0.123
r_gen_planes_refined	0.014
r_bond_refined_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2749
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.