5MFZ

Human Sirt6 in complex with small molecule UBCS40

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MF6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	293	1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.364	α = 90
b = 91.364	β = 90
c = 144.212	γ = 120

Symmetry
Space Group	P 63

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		2016-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.1	48.07	99.7	0.161	12.89	11.4		39828		2.33

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.22	98		1.095		11.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5MF6	2.1	45.68	37793	2032	99.74	0.16933	0.16726	0.20806	RANDOM	39.104

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]
-11.91			-11.91		23.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.692
r_dihedral_angle_4_deg	19.866
r_dihedral_angle_3_deg	15.787
r_long_range_B_refined	8.801
r_long_range_B_other	8.8
r_dihedral_angle_1_deg	7.249
r_scangle_other	6.899
r_mcangle_it	5.422
r_mcangle_other	5.421
r_scbond_it	4.925
r_scbond_other	4.924
r_mcbond_other	4.054
r_mcbond_it	4.053
r_angle_refined_deg	2.447
r_angle_other_deg	1.274
r_chiral_restr	0.14
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_bond_other_d	0.006
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4337
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	142

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing