6XVG | pdb_00006xvg

Human Sirt6 3-318 in complex with ADP-ribose and the activator MDL-801

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K35

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.51	α = 90
b = 136.534	β = 117.71
c = 89.873	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 PILATUS3 2M		2019-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.1	46.39	99.4	0.13	0.999	15.7	14		110958			51.46

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.23	97.6		2.4	0.499	1.1	14.3

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	3K35	2.1	46.39	108840	2101	99.6	0.2049	0.2044	0.21	0.2298	0.23	RANDOM	53.293

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]
-2.55		-0.48	1.69		0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.398
r_dihedral_angle_4_deg	18.55
r_dihedral_angle_3_deg	13.657
r_dihedral_angle_1_deg	6.185
r_angle_refined_deg	1.484
r_angle_other_deg	1.322
r_chiral_restr	0.069
r_gen_planes_other	0.009
r_bond_refined_d	0.008
r_gen_planes_refined	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.398
r_dihedral_angle_4_deg	18.55
r_dihedral_angle_3_deg	13.657
r_dihedral_angle_1_deg	6.185
r_angle_refined_deg	1.484
r_angle_other_deg	1.322
r_chiral_restr	0.069
r_gen_planes_other	0.009
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12939
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	539

Software

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

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.