9VG0 | pdb_00009vg0

SIRT2 structure in complex with H3K18myr peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4X3O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	Tris 8.0, 25% PEG 2000MME

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.152	α = 90
b = 73.504	β = 94.087
c = 55.731	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 EIGER X 16M		2024-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97918	SSRF	BL10U2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.61	55.59	91.8	0.997	17.1	6.4		34600

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.61	1.64			0.939

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4X3O	1.61	27.81	34572	1746	91.681	0.191	0.1883	0.1961	0.2313	0.2307	25.83

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]
-0.348		1.88	-0.606		0.678

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.277
r_dihedral_angle_4_deg	20.29
r_dihedral_angle_3_deg	15.832
r_dihedral_angle_1_deg	6.812
r_lrange_it	4.896
r_lrange_other	4.882
r_scangle_it	3.226
r_scangle_other	3.226
r_scbond_it	2.168
r_scbond_other	2.167
r_mcangle_it	1.993
r_mcangle_other	1.993
r_angle_refined_deg	1.903
r_angle_other_deg	1.49
r_mcbond_it	1.39
r_mcbond_other	1.388
r_nbd_refined	0.238
r_nbd_other	0.192
r_symmetry_nbd_other	0.188
r_symmetry_nbd_refined	0.184
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.152
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2271
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	36

Software

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