6EO0

Zebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4UTV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	20% PEG8000, 0.2 M MgCl2, 0.1 M Tris/HCl pH 8.5, 0.1 M glycine

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.93	α = 90
b = 113.59	β = 103.24
c = 72.31	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 2M-F		2016-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.918400	SLS	X06DA

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	2.4	50	96.2	0.252	0.989	6.1	3.8		38453

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	2.4	2.5	97.3		1.702	0.517	0.9	3.8

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	4UTV	2.4	48.41	36530	1923	96.26	0.25531	0.25263	0.30492	RANDOM	52.227

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]
0.83		1.44	-1.63		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.805
r_dihedral_angle_3_deg	18.062
r_dihedral_angle_4_deg	16.815
r_dihedral_angle_1_deg	6.542
r_long_range_B_refined	6.122
r_long_range_B_other	6.115
r_mcangle_it	3.328
r_mcangle_other	3.328
r_scangle_other	3.078
r_mcbond_it	2.032
r_mcbond_other	2.032
r_scbond_it	1.983
r_scbond_other	1.983
r_angle_refined_deg	1.967
r_angle_other_deg	1.3
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.005
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	8541
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	420

Software

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