Experiment: 5HI7

Co-crystal structure of human SMYD3 with an aza-SAH compound

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	SMYD3 crystallization and soaking of GSK2807: SMYD3 (1-428) expressed in baculovirus and with SAH in the SAM-binding site was crystallized in sitting drops at 22C using 1uL fresh protein at 8.9mg/mL with the addition of 1uL mother liquor (200mM MgOAc Tetrahydrate, 20% PEG 3350). Crystals grew to a large size but varied in quantity when set up in replicates. A seed stock was formed from these crystals and added at 20% to the mother liquor solution prior to plate setup. Crystals of large size were then created with 1.3uL protein and 1.3uL of mother liquor containing seeds in a sitting drop MRC-2 plate (Hampton Research). Crystal nucleation occurred overnight and reached maximum size in 4 days

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.47	α = 90
b = 66.401	β = 90
c = 104.851	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	CCD	MARMOSAIC 300 mm CCD		2013-01-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07820	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	50	99.2	11.4	2.2		46288			26.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.15	44.709	1.35	23433	1211	99.17	0.1999	0.1984	0.2021	0.2257	0.2293	random selection	36

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
f_dihedral_angle_d	11.897
f_angle_d	0.626
f_chiral_restr	0.037
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3259
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	39

Software

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