4L3O | pdb_00004l3o

Crystal Structure of SIRT2 in complex with the macrocyclic peptide S2iL5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J8F	PDB entry 1J8F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	8.5% PEG 4000, 0.1M MES-NaOH, 0.1M Li2SO4, 0.1M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.18	α = 90
b = 135.613	β = 90
c = 148.83	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD			2012-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.000	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.518	50					61389			27.09

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entry 1J8F	2.518	46.59	1.5	61346	6136	97.13	0.2162	0.211	0.2071	0.2629	0.2584	35.9615

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]
5.8184			-1.0871		-4.7313

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.79
f_angle_d	0.619
f_chiral_restr	0.046
f_bond_d	0.003
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9899
Nucleic Acid Atoms
Solvent Atoms	507
Heterogen Atoms	68

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction