9VGZ | pdb_00009vgz

SIRT2-F96A structure in complex with H3K18myr peptide and native NAD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9VEM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	Tris 8.0, 25% PEG 2000MME

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.915	α = 90
b = 77.134	β = 97.107
c = 56.155	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		2024-12-29	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	2.34	45.21	91.2	0.995	15.3	5.3		12400

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	2.34	2.42			0.965

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	9VEM	2.34	45.21	12377	567	90.894	0.181	0.1788	0.1836	0.2356	0.2368	43.592

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]
1.209		2.402	-0.756		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.268
r_dihedral_angle_6_deg	14.71
r_dihedral_angle_2_deg	9.027
r_dihedral_angle_1_deg	6.871
r_lrange_it	6.811
r_lrange_other	6.811
r_scangle_it	5.205
r_scangle_other	5.203
r_mcangle_it	3.458
r_mcangle_other	3.457
r_scbond_it	3.393
r_scbond_other	3.392
r_mcbond_it	2.372
r_mcbond_other	2.37
r_angle_refined_deg	1.754
r_angle_other_deg	0.572
r_dihedral_angle_other_2_deg	0.241
r_nbd_other	0.229
r_nbd_refined	0.227
r_symmetry_nbd_other	0.207
r_xyhbond_nbd_refined	0.195
r_metal_ion_refined	0.195
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.137
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2334
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	71

Software

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