6ZRB | pdb_00006zrb

Crystal structure of SMYD3 conjugate with piperidine-based covalent inhibitor EM127

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	8.25	298	Protein was pre-incubated with the covalent inhibitor, 7 mg/mL and 0.4 mM, respectively, for 8 h at RT. Crystallization was performed in 2 uL hanging drops, 1:1 protein to reservoir ratio, reservoir: 16% PEG3350, 100 mM Tris (pH 8.25), 100 mM Mg(OAc)2). Protein crystals were cryoprotected in 20% PEG3350, 100 mM Tris (pH 8.25), 100 mM Mg(OAc)2, 10% DMSO and 10% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.935	α = 90
b = 65.989	β = 90
c = 107.318	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 EIGER X 16M		2019-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.918	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.55	107.32	98.7	0.052	0.057	0.025	0.999	16.4	5		62691

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	1.55	1.58	86.6		0.45	0.532	0.277	0.789	2.3	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	THROUGHOUT	6Z2R	1.55	56.28	59518	3106	98.58	0.1664	0.1654	0.18	0.1845	0.2	RANDOM	21.465

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]
1.14			-0.39		-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.973
r_dihedral_angle_4_deg	15.346
r_dihedral_angle_3_deg	13.64
r_dihedral_angle_1_deg	6.093
r_angle_other_deg	2.316
r_mcangle_it	2.206
r_angle_refined_deg	1.517
r_mcbond_other	1.402
r_mcbond_it	1.401
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.973
r_dihedral_angle_4_deg	15.346
r_dihedral_angle_3_deg	13.64
r_dihedral_angle_1_deg	6.093
r_angle_other_deg	2.316
r_mcangle_it	2.206
r_angle_refined_deg	1.517
r_mcbond_other	1.402
r_mcbond_it	1.401
r_chiral_restr	0.083
r_bond_other_d	0.035
r_gen_planes_other	0.011
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3402
Nucleic Acid Atoms
Solvent Atoms	412
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

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.