3F9Y

Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me1 / AdoHcy

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.4	α = 91.4
b = 45	β = 115.3
c = 52.4	γ = 89.8

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	CCD	MARMOSAIC 300 mm CCD		2006-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.5	25		0.067	22.5	7.8		55907		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.6			0.528	8.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1ZKK	1.5	23.68	2	53407	2811	100	0.19497	0.19364	0.22012	RANDOM	32.444

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]
-0.25	-0.05	0.1	0.21		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.569
r_dihedral_angle_4_deg	17.717
r_dihedral_angle_3_deg	14.017
r_dihedral_angle_1_deg	6.543
r_scangle_it	4.082
r_scbond_it	2.794
r_angle_refined_deg	1.895
r_mcangle_it	1.862
r_mcbond_it	1.216
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.569
r_dihedral_angle_4_deg	17.717
r_dihedral_angle_3_deg	14.017
r_dihedral_angle_1_deg	6.543
r_scangle_it	4.082
r_scbond_it	2.794
r_angle_refined_deg	1.895
r_mcangle_it	1.862
r_mcbond_it	1.216
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.205
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.123
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2680
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	52

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	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.