2OT7 | pdb_00002ot7

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

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, 100 mM Citrate, 2 mM NiCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.209	α = 90
b = 149.842	β = 90
c = 57.47	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	ADSC QUANTUM 315		2007-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0723	ESRF	ID23-1

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	2.135	83.92	99.1	0.072	11.9	2.9	48784	48784			38

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	2.135	2.25	100		0.541	2	3	7095

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	2.135	20	45914	45914	2031	97.2	0.18909	0.18909	0.18676	0.19	0.24072	0.25	RANDOM	32.416

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]
-0.97			0.04		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.971
r_dihedral_angle_3_deg	14.422
r_dihedral_angle_4_deg	14.22
r_dihedral_angle_1_deg	6.566
r_scangle_it	6.362
r_scbond_it	5.165
r_mcangle_it	3.331
r_mcbond_it	2.384
r_angle_refined_deg	1.33
r_angle_other_deg	0.897
r_mcbond_other	0.632
r_symmetry_vdw_other	0.252
r_symmetry_hbond_refined	0.232
r_symmetry_vdw_refined	0.198
r_nbd_refined	0.196
r_nbd_other	0.183
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.157
r_nbtor_other	0.085
r_chiral_restr	0.077
r_metal_ion_refined	0.039
r_bond_refined_d	0.012
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_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	5730
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	24

Software

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