3FLG | pdb_00003flg

The PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 beta

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KHC	PDB entry 1KHC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		Purified DNMT3B was crystallized using sitting drop vapor diffusion method at 20 C by mixing 1 ul of the protein solution with 1 ul of the reservoir solution containing 30% PEG 2,000 MME, 0.2 M KBr, pH 7.5, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.17	α = 90
b = 75.062	β = 90
c = 34.488	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	100					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	1.54178

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	1.8	50	99.7	0.059	22.974	6.8		13589

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)
	1.8	1.86	100		0.123		6.7	1329

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	PDB entry 1KHC	1.8	43.94	13555	669	99.65	0.206	0.204	0.2011	0.244	0.2388	RANDOM	23.454

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]
0.78			0.37		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.197
r_dihedral_angle_3_deg	14.998
r_dihedral_angle_4_deg	8.16
r_dihedral_angle_1_deg	5.776
r_scangle_it	3.715
r_scbond_it	2.682
r_mcangle_it	1.732
r_angle_refined_deg	1.482
r_mcbond_it	1.151
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.211
r_nbd_refined	0.203
r_symmetry_hbond_refined	0.201
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1058
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction