2OQ6 | pdb_00002oq6

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5	277	0.1 M citrate, 4mM NiCl2, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 5.50

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.347	α = 90
b = 149.88	β = 90
c = 57.26	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		2006-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		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	2	45.5	99.9	0.085	0.094	13.5	5.6		59834		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	2	2.11	99.7		0.837	0.919	2.1	5.5

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	2	41.96	57260	57260	2514	99.9	0.16478	0.16478	0.16286	0.17	0.20773	0.21	RANDOM	33.18

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]
-0.23			-0.08		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.773
r_dihedral_angle_3_deg	13.976
r_dihedral_angle_4_deg	13.233
r_scangle_it	8.393
r_scbond_it	6.514
r_dihedral_angle_1_deg	6.234
r_mcangle_it	4.558
r_mcbond_it	3.564
r_angle_refined_deg	1.349
r_mcbond_other	1.004
r_angle_other_deg	0.922
r_symmetry_hbond_refined	0.265
r_symmetry_vdw_other	0.227
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.197
r_nbd_other	0.185
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.155
r_nbtor_other	0.085
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
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	5722
Nucleic Acid Atoms
Solvent Atoms	389
Heterogen Atoms	24

Software

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