4HP3 | pdb_00004hp3

Crystal structure of Tet3 in complex with a CpG dsDNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		unpublished model of complex between same protein construct and a methylated DNA fragment. That structure was solved by a combination of zinc-SAD (SHELXD/E) and molecular replacement in ""density"" mode (MOLREP), using ideal DNA (COOT) and human MLL2 (currently unpublished) as search models.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.892	α = 90
b = 39.455	β = 99.92
c = 54.134	γ = 90

Symmetry
Space Group	C 1 2 1

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 300 mm CCD		2012-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-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	2.05	34.42	99.79	0.053	12.5727	3.71		9281

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	2.05	2.16	99.85		0.67		3.71	1345

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	unpublished model of complex between same protein construct and a methylated DNA fragment. That structure was solved by a combination of zinc-SAD (SHELXD/E) and molecular replacement in "density" mode (MOLREP), using ideal DNA (COOT) and human MLL2 (currently unpublished) as search models.	2.05	30	9281	452	99.678	0.217	0.2155	0.2195	0.2434	0.2563	RANDOM	52.769

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]
-1		0.395	-0.739		1.875

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.342
r_dihedral_angle_4_deg	20.48
r_dihedral_angle_3_deg	14.94
r_dihedral_angle_1_deg	6.013
r_angle_refined_deg	1.359
r_angle_other_deg	1.16
r_chiral_restr	0.064
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	384
Nucleic Acid Atoms	486
Solvent Atoms	23
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction