2OX0 | pdb_00002ox0

Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	0.1M Citrate, 4mM NiCl2, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.21	α = 90
b = 150.004	β = 90
c = 57.228	γ = 90

Symmetry
Space Group	P 21 21 2

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		2007-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.91820	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.95	41.49	99.6	0.072	0.084	12	3.6	64355	64097		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.06	98.4		0.589	0.699	2	3.3	9121

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.95	41.49	61370	61370	2679	99.49	0.17047	0.17047	0.16871	0.1748	0.20999	0.2126	RANDOM	29.491

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]
-0.8			-0.12		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.61
r_dihedral_angle_4_deg	13.077
r_dihedral_angle_3_deg	12.843
r_dihedral_angle_1_deg	5.924
r_scangle_it	5.276
r_scbond_it	3.801
r_mcangle_it	2.584
r_mcbond_it	1.802
r_angle_refined_deg	1.139
r_angle_other_deg	0.857
r_mcbond_other	0.481
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.191
r_nbtor_refined	0.181
r_nbd_other	0.178
r_symmetry_vdw_other	0.165
r_xyhbond_nbd_refined	0.127
r_symmetry_vdw_refined	0.103
r_nbtor_other	0.087
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5737
Nucleic Acid Atoms
Solvent Atoms	483
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing