4UTZ

Crystal structure of zebrafish Sirtuin 5 in complex with adipoylated CPS1-peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NYR	PDB ENTRY 2NYR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		22% PEG3350, 0.1 M HEPES PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.9	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.32	α = 90
b = 87.32	β = 90
c = 314.57	γ = 120

Symmetry
Space Group	P 65 2 2

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	MIRRORS	2013-07-05	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.3	50	99.9	0.33	9.1	10		11477		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.4	100		1.26	2.4	10.4

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2NYR	3.3	48.41	10881	595	99.87	0.21173	0.20934	0.25437	RANDOM	67.559

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]
0.65	0.32		0.65		-2.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.382
r_dihedral_angle_4_deg	17.426
r_dihedral_angle_3_deg	17.185
r_dihedral_angle_1_deg	6.864
r_mcangle_it	3.417
r_scbond_it	2.098
r_mcbond_it	2.009
r_mcbond_other	2.009
r_angle_refined_deg	1.687
r_angle_other_deg	1.164
r_chiral_restr	0.103
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.003
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4125
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing