Experiment: 3Q0D

Crystal structure of SUVH5 SRA- hemi methylated CG DNA complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SRA Molecule from the SUVH5 SRA-fully methylated Cg DNA crystallized in space group P42212

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	19% PEG4000, 100 mM MES, pH 6.5, 200 mM NaCl and 3 mM spermine, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.379	α = 90
b = 76.379	β = 90
c = 74.254	γ = 90

Symmetry
Space Group	P 42

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	Cryogenecally-cooled double Si(111) monochromoter		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97918	APS	24-ID-C

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	2.37	20	98.8	0.07	0.068	30.1	7.3	17443	17234

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	SRA Molecule from the SUVH5 SRA-fully methylated Cg DNA crystallized in space group P42212	2.3704	19.095	1.39	17221	873	98.78	0.2265	0.2246	0.219	0.2628	0.2565

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]
1.8426			1.8426		-7.7466

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	22.458
f_angle_d	1.378
f_chiral_restr	0.082
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2173
Nucleic Acid Atoms	405
Solvent Atoms	51
Heterogen Atoms	1

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling