Experiment: 7QNR

SMYD3 in complex with fragment FL01791

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
2.12	42.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.236	α = 90
b = 66.218	β = 90
c = 105.302	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 PILATUS3 6M		2021-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.965459	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.57	44.56	97.8	0.1338	0.07183	0.996	7.03	4		233855			22.49

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.57	1.626			2.605	1.373	0.171	0.5

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	1.57	44.56	1.03	106759	2090	93.02	0.2041	0.2035	0.2025	0.2348	0.2354	29.62

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	20.9962
f_angle_d	0.8277
f_chiral_restr	0.045
f_plane_restr	0.0196
f_bond_d	0.0061

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3408
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	39

Software

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