9VG3 | pdb_00009vg3

SIRT2 structure in complex with H3K18myr peptide: pre NAD binding state

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	8	289	Tris 8.0, 25% PEG2000MME

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.508	α = 90
b = 72.528	β = 95.27
c = 53.921	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	2.15	53.751	99	0.997	11.9	6.9		14755

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	2.15	2.21			0.876

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	2.15	53.751	14728	739	98.779	0.199	0.1963	0.2033	0.2511	0.2456	47.31

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]
-2.939		0.346	-0.407		3.227

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.952
r_dihedral_angle_3_deg	16.94
r_dihedral_angle_6_deg	14.464
r_dihedral_angle_1_deg	6.634
r_lrange_other	3.516
r_lrange_it	3.514
r_scangle_it	2.274
r_scangle_other	2.274
r_mcangle_it	2.142
r_mcangle_other	2.142
r_angle_refined_deg	1.573
r_scbond_it	1.537
r_scbond_other	1.536
r_mcbond_it	1.511
r_mcbond_other	1.51
r_angle_other_deg	0.528
r_nbd_other	0.264
r_symmetry_xyhbond_nbd_refined	0.263
r_symmetry_nbd_other	0.217
r_xyhbond_nbd_other	0.217
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.2
r_symmetry_nbd_refined	0.187
r_nbtor_refined	0.181
r_metal_ion_refined	0.139
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.049
r_bond_refined_d	0.006
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	2311
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	24

Software

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