9VH0 | pdb_00009vh0

SIRT2-H187A structure in complex with H3K18myr peptide and native NAD

X-RAY DIFFRACTION

---

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	5.5	289	0.1 M MES 5.5, 9.2% PEG10000

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.434	α = 100.187
b = 48.13	β = 91.579
c = 96.194	γ = 112.167

Symmetry
Space Group	P 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 PILATUS3 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	2.41	47.13	92.1	0.995	8.9	3.7		21638

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	2.41	2.5			0.809

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	2.41	47.129	21622	1083	92.056	0.201	0.1976	0.2069	0.2733	0.2807	46.165

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]
-0.979	0.71	-2.658	-0.164	-4.357	3.359

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.773
r_dihedral_angle_6_deg	14.016
r_dihedral_angle_2_deg	10.863
r_lrange_it	8.807
r_lrange_other	8.807
r_dihedral_angle_1_deg	7.756
r_scangle_it	6.16
r_scangle_other	6.159
r_mcangle_it	5.889
r_mcangle_other	5.889
r_scbond_it	3.957
r_scbond_other	3.956
r_mcbond_it	3.894
r_mcbond_other	3.893
r_angle_refined_deg	1.656
r_dihedral_angle_other_2_deg	0.842
r_angle_other_deg	0.568
r_symmetry_xyhbond_nbd_refined	0.296
r_nbd_other	0.24
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.212
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_other	0.113
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.077
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	4571
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	120

Software

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