2Q8D

Crystal structure of JMJ2D2A in ternary complex with histone H3-K36me2 and succinate

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.857	α = 90
b = 148.642	β = 90
c = 57.346	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	200	CCD	MARMOSAIC 300 mm CCD		2007-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.00	APS	23-ID-D

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	2.29	37.8		0.09	0.073	36.1	4.7		38447	2	1

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)
	2.29	2.38			0.471	0.452	2.7	3	1099

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2GP5	2.29	37.8	1	2	38402	1927	97	0.20602	0.20362	0.25057	RANDOM	36.28

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]
-0.32			-0.35		0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.968
r_dihedral_angle_4_deg	19.5
r_dihedral_angle_3_deg	17.724
r_dihedral_angle_1_deg	5.825
r_scangle_it	2.16
r_scbond_it	1.408
r_angle_refined_deg	1.294
r_mcangle_it	0.943
r_mcbond_it	0.539
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.252
r_symmetry_vdw_refined	0.2
r_nbd_refined	0.196
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5672
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing