2OQ7

The crystal structure of JMJD2A complexed with Ni and N-oxalylglycine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GP3	PDB entry 2gp3

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.12	α = 90
b = 148.531	β = 90
c = 57.333	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		2006-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99900	SLS	X10SA

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	2.15	59.87	94.5	0.078	10.4	3.2	45023	45023			36

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	2.15	2.27	96.5		0.485	2.1	3.2	6601

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 2gp3	2.15	50	43072	43072	1912	94.06	0.17876	0.17876	0.17654	0.228	RANDOM	29.938

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]
-0.35			-0.8		1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.465
r_dihedral_angle_4_deg	17.523
r_dihedral_angle_3_deg	15.496
r_scangle_it	7.292
r_dihedral_angle_1_deg	6.832
r_scbond_it	6.068
r_mcangle_it	3.972
r_mcbond_it	2.9
r_angle_refined_deg	1.583
r_angle_other_deg	0.981
r_mcbond_other	0.841
r_symmetry_hbond_refined	0.231
r_symmetry_vdw_other	0.209
r_nbd_refined	0.199
r_nbd_other	0.191
r_nbtor_refined	0.186
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.095
r_nbtor_other	0.091
r_metal_ion_refined	0.064
r_bond_refined_d	0.017
r_xyhbond_nbd_other	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	5536
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling