3UT1 | pdb_00003ut1

Crystal structure of the 3-MBT repeat domain of L3MBTL3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OYX	based on unpublished model of L3MBTL1, itself based on molecular replacement with coordinates from PDB entry 1OYX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	291	27% PEG-3350, 0.1M ammonium sulfate, 0.2M cobaltous chloride, 0.1M Bis-tris, pH 5.5, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.287	α = 90
b = 70.619	β = 119.95
c = 58.574	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 270		2011-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.9179	CHESS	F1

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	50	99.9	0.13	6.1	5.4		20483

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	2.12	99.5		0.859		4.5	2031

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X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	based on unpublished model of L3MBTL1, itself based on molecular replacement with coordinates from PDB entry 1OYX	2.05	44.761	20448	1028	99.446	0.224	0.222	0.2281	0.267	0.2696	RANDOM	27.696

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]
-1.043		-1.888	-1.478		0.636

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.125
r_dihedral_angle_4_deg	16.277
r_dihedral_angle_3_deg	13.149
r_dihedral_angle_1_deg	5.997
r_angle_refined_deg	1.309
r_angle_other_deg	0.847
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2463
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	32

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling