Experiment: 7QNU

SMYD3 in complex with fragment FL08619

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Z2R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.1 M Tris pH 8.25-8.75 0.1M Magnesium acetate 15-18 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.931	α = 90
b = 65.886	β = 90
c = 105.085	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	PIXEL	DECTRIS PILATUS 6M		2021-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.976256	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.64	41.08	74.97	0.2142	0.991	6.45	6.2		48981			16.27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.699			1.548	0.134

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6z2r	1.64	41.08	1.34	38744	1987	74.23	0.1869	0.1846	0.1912	0.2295	0.2327	23.61

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	21.7871
f_angle_d	0.8744
f_chiral_restr	0.0504
f_plane_restr	0.0116
f_bond_d	0.0085

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3408
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	41

Software

Software
Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
Aimless	data scaling
PHASER	phasing