Experiment: 5CCL

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.10 M Magnesium formate, 0.1M Tris 8.0, 14% w/v PEG 3350. Crystals of SMYD3-SAM were produced and compound was soaked into the pre-formed crystals

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.594	α = 90
b = 65.232	β = 90
c = 105.966	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	100	CCD	ADSC QUANTUM 315r		2014-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97907	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	55.55	94.4	0.069	0.077	0.033	14.6	5		62186

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	98.6		0.226	0.253	0.111	0.948		4.9	6399

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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		THROUGHOUT	1.5	55.55	59053	3081	94.29	0.1159	0.1134	0.1643	RANDOM	22.997

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]
0.61			-0.56		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.614
r_sphericity_free	23.573
r_dihedral_angle_4_deg	19.865
r_dihedral_angle_3_deg	14.196
r_sphericity_bonded	11.646
r_dihedral_angle_1_deg	6.11
r_mcangle_it	3.787
r_mcbond_it	3.367
r_mcbond_other	3.367
r_rigid_bond_restr	3.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.614
r_sphericity_free	23.573
r_dihedral_angle_4_deg	19.865
r_dihedral_angle_3_deg	14.196
r_sphericity_bonded	11.646
r_dihedral_angle_1_deg	6.11
r_mcangle_it	3.787
r_mcbond_it	3.367
r_mcbond_other	3.367
r_rigid_bond_restr	3.323
r_angle_refined_deg	1.732
r_angle_other_deg	0.913
r_chiral_restr	0.124
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3400
Nucleic Acid Atoms
Solvent Atoms	449
Heterogen Atoms	73

Software

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

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.