3A1A

Crystal Structure of the DNMT3A ADD domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	17% PEG 8000, 0.1M Tris-HCl, 0.2M magnesium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.581	α = 90
b = 57.581	β = 90
c = 138.949	γ = 120

Symmetry
Space Group	P 61 2 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	mirrors	2007-10-19	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315	mirrors	2007-10-19	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.28221, 1.28333, 1.25730, 1.29001	Photon Factory	BL-5A

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	2.3	28.796	98.9	0.063	16.4	12.3	6567	6551	1	1

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	2.3	2.38	99.2		0.41		12.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2.3	28.79	6245	306	99.42	0.21113	0.20938	0.24968	RANDOM	45.477

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]
0.17	0.09		0.17		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.672
r_dihedral_angle_4_deg	20.497
r_dihedral_angle_3_deg	16.831
r_dihedral_angle_1_deg	6.224
r_scangle_it	1.999
r_scbond_it	1.419
r_angle_refined_deg	1.316
r_mcangle_it	0.825
r_mcbond_it	0.463
r_nbtor_refined	0.302
r_nbd_refined	0.203
r_symmetry_hbond_refined	0.193
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1035
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing