2OS2 | pdb_00002os2

Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys36

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OQ7	PDB entry 2oq7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	20% PEG 3350, 0.1 M Citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.943	α = 90
b = 148.886	β = 90
c = 56.975	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	IMAGE PLATE	RIGAKU RAXIS HTC		2007-01-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54180

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	2.3	30	98.4	0.059	20	3.8	38324	38324			47

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	93.3		1.9	3.6	5187

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 (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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 2oq7	2.3	30	36665	36665	1608	98.17	0.17863	0.17863	0.17649	0.1798	0.22552	0.2261	RANDOM	29.484

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]
-1.17			0.07		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.405
r_dihedral_angle_4_deg	16.941
r_dihedral_angle_3_deg	14.552
r_scangle_it	7.436
r_scbond_it	6.388
r_dihedral_angle_1_deg	6.314
r_mcangle_it	4.117
r_mcbond_it	3.068
r_angle_refined_deg	1.4
r_angle_other_deg	0.93
r_mcbond_other	0.45
r_symmetry_hbond_refined	0.211
r_symmetry_vdw_other	0.187
r_nbd_other	0.186
r_nbd_refined	0.185
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.149
r_symmetry_vdw_refined	0.126
r_nbtor_other	0.087
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
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	5740
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	24

Software

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