7T1D

Human SIRT2 in complex with small molecule 359

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		reference structure of SIRT2 from the company CRELUX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293.15	Crystals of SIRT2 in complex with FLS-359 were obtained using hanging-drop vapour diffusion setups. SIRT2 at a concentration of 21.9 mg/ml (50 mM Hepes-NaOH, 150 mM NaCl, pH 8.0) was preincubated with 3.6 mM (5.7-fold molar excess) of FLS-359 (100 mM in DMSO) for 1 h. 1 ul of the protein solution was then mixed with 2 ul of reservoir solution (0.1 M Hepes-NaOH pH 6.6, 0.3 M Li2SO4, 21 % (w/v) PEG 3350) and streak seeded before being equilibrated at 20C over 0.2 ml of reservoir solution. Well diffracting crystals grew as thick aggregates of thin plates and were mounted within 19 days

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.775	α = 90
b = 55.98	β = 94.462
c = 139.576	γ = 90

Symmetry
Space Group	P 1 21 1

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-F		2020-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	1.0332	ESRF	MASSIF-1

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	1.75	139.15	98.6	0.075	0.089	0.047	0.996	9.5	3.5		56312

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	1.75	1.78	98.9		0.612	0.727	0.388	0.664		3.4

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	CRELUX reference structure of SIRT2	1.75	35.002	56285	2843	98.316	0.166	0.163	0.2128	RANDOM	25.623

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]
0.054		0.172	-0.358		0.274

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.859
r_dihedral_angle_4_deg	19.024
r_dihedral_angle_3_deg	14.127
r_lrange_it	7.101
r_lrange_other	6.948
r_dihedral_angle_1_deg	6.89
r_scangle_it	4.178
r_scangle_other	4.178
r_mcangle_other	3.28
r_mcangle_it	3.279
r_scbond_it	2.801
r_scbond_other	2.8
r_mcbond_it	2.221
r_mcbond_other	2.221
r_angle_refined_deg	1.574
r_angle_other_deg	1.364
r_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.203
r_xyhbond_nbd_refined	0.191
r_symmetry_nbd_other	0.184
r_nbd_other	0.182
r_nbtor_refined	0.168
r_symmetry_nbd_refined	0.147
r_ncsr_local_group_1	0.107
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.06
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4701
Nucleic Acid Atoms
Solvent Atoms	681
Heterogen Atoms	126

Software

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