6FKY | pdb_00006fky

Crystal structure of zebrafish Sirtuin 5 in complex with 3-(benzylthio)succinyl-CPS1 peptide

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, HANGING DROP	7.5	293	0.1 M HEPES pH 7.4, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.134	α = 90
b = 87.134	β = 90
c = 316.677	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 2M	MIRRORS	2016-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

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	2.98	50	99.8	0.358	0.994	9.8	15.5		15459

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	2.98	3.16	99.1		2.1	0.513	1.3	16

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	4utv	2.98	48.51	14686	773	99.77	0.20163	0.19785	0.2	0.27485	0.28	RANDOM	67.667

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]
0.22	0.11		0.22		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.391
r_dihedral_angle_4_deg	20.627
r_dihedral_angle_3_deg	18.049
r_long_range_B_refined	7.586
r_long_range_B_other	7.583
r_dihedral_angle_1_deg	6.543
r_scangle_other	5.166
r_mcangle_it	4.998
r_mcangle_other	4.997
r_scbond_it	3.182
r_scbond_other	3.182
r_mcbond_it	3.015
r_mcbond_other	3.015
r_angle_refined_deg	1.872
r_angle_other_deg	1.099
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
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	4232
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	52

Software

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