8AKC | pdb_00008akc

Human Sirt6 in complex with ADP-ribose and fragment 3-(acetylamino)thiophene-2-carboxylic acid

X-RAY DIFFRACTION

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
2.6	52.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.071	α = 90
b = 91.071	β = 90
c = 143.588	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 2M		2017-09-05	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	1.83	45.54	99.9	0.17	0.995	7.25	6.9		59281			37.779

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	1.83	1.94	99.9		2.01	0.345	0.82	7.2

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	5MF6	1.83	45.54	57141	2139	99.9	0.1883	0.1876	0.19	0.2063	0.21	RANDOM	38.294

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]
-14			-14		28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.418
r_dihedral_angle_4_deg	20.774
r_dihedral_angle_3_deg	15.712
r_dihedral_angle_1_deg	6.86
r_angle_refined_deg	1.61
r_angle_other_deg	1.275
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.418
r_dihedral_angle_4_deg	20.774
r_dihedral_angle_3_deg	15.712
r_dihedral_angle_1_deg	6.86
r_angle_refined_deg	1.61
r_angle_other_deg	1.275
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4360
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	159

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	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.