6CCG

Crystal structure MBD3 MBD domain in complex with methylated CpG DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	15% PEG 8000,0.2M magnesium chloride, 0.1M Tris

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.27	α = 90
b = 36.46	β = 92.42
c = 130.84	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	ADSC QUANTUM 315		2012-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97911	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.9	35.18	99.9	0.068	0.074	0.029	0.999	16.7	5.7		27299

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	99.8		1.098	1.285	0.662	0.615		3.7	1749

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	FOURIER SYNTHESIS	THROUGHOUT	1.9	35.1	25763	1536	99.84	0.2247	0.2232	0.2501	thin shells (sftools)	43.018

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]
-1.14		0.33	1.39		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.59
r_dihedral_angle_4_deg	16.751
r_dihedral_angle_3_deg	10.306
r_dihedral_angle_1_deg	5.368
r_mcangle_it	2.202
r_angle_refined_deg	1.543
r_mcbond_other	1.362
r_mcbond_it	1.361
r_angle_other_deg	1.19
r_chiral_restr	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1144
Nucleic Acid Atoms	976
Solvent Atoms	88
Heterogen Atoms	10

Software

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