9VEW | pdb_00009vew

SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 2

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
2.36	47.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.919	α = 90
b = 76.608	β = 97.363
c = 55.707	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 6M		2025-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97861	SSRF	BL19U1

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	2.68	55.31	98.8	0.995	10.6	6.9		8852

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	2.68	2.81			0.922	3.4

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 (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	2.68	55.309	8784	431	98.069	0.186	0.1823	0.1874	0.2507	0.2471	45.752

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]
-1.733		0.293	3.435		-1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.241
r_dihedral_angle_6_deg	14.902
r_dihedral_angle_2_deg	8.177
r_dihedral_angle_1_deg	7.701
r_lrange_it	5.905
r_lrange_other	5.9
r_scangle_it	3.455
r_scangle_other	3.454
r_mcangle_it	3.152
r_mcangle_other	3.151
r_scbond_it	2.235
r_scbond_other	2.234
r_mcbond_it	1.962
r_mcbond_other	1.962
r_angle_refined_deg	1.643
r_dihedral_angle_other_2_deg	0.69
r_angle_other_deg	0.559
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.226
r_symmetry_nbd_refined	0.215
r_symmetry_nbd_other	0.211
r_nbtor_refined	0.189
r_nbd_other	0.177
r_symmetry_xyhbond_nbd_refined	0.137
r_metal_ion_refined	0.101
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.086
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2261
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	74

Software

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