2RHU | pdb_00002rhu

Crystal structure of the 3-MBT repeats from human L3MBTL1 bound to dimethyl-lysine and in chimera with histone H3.3(28-34)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OZ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	Crystals was generated by pre-incubating the L3MBTL1-H3.3(28-34) (18MG/ML IN 50MM KCL, 25MM TRIS-HCL PH 8.0, 1MM DTT) with a five-fold molar excess of dimethyl-lysine amino acid. Drops were prepared by mixing equal volumes of the complex with reservoir solution (5% PEG10K, 0.1 M Tris-maleate pH 6.5, 0.1 M ammonium sulfate), VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.166	α = 90
b = 94.023	β = 90
c = 59.187	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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2007-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.54

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	1.9	20	100	0.068	0.068	26.8	6.4	38237	38237	-3	-3	33.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.97	100		0.414	0.414	5	6.3	3764

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	1OZ2	1.9	20	38146	37183	2232	97.5	0.194	0.18	0.215	0.2	random	29

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1.49
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2623
Nucleic Acid Atoms
Solvent Atoms	529
Heterogen Atoms	30

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.