9VEM | pdb_00009vem

SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 1

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	47.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.859	α = 90
b = 76.409	β = 97.293
c = 55.64	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	2.57	55.251	99.2	0.991	7.1	6.9		10021

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	2.57	2.68			0.767

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	2.57	55.251	9950	495	98.417	0.19	0.1867	0.192	0.2642	0.2692	46.722

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]
-0.424		0.588	0.768		-0.479

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.703
r_dihedral_angle_6_deg	13.025
r_dihedral_angle_1_deg	7.145
r_dihedral_angle_2_deg	7.023
r_lrange_it	5.081
r_lrange_other	5.08
r_scangle_it	2.79
r_scangle_other	2.789
r_mcangle_it	2.574
r_mcangle_other	2.573
r_scbond_it	1.773
r_scbond_other	1.772
r_mcbond_it	1.556
r_mcbond_other	1.556
r_angle_refined_deg	1.498
r_angle_other_deg	0.513
r_dihedral_angle_other_2_deg	0.46
r_nbd_refined	0.224
r_nbd_other	0.21
r_symmetry_nbd_other	0.209
r_metal_ion_refined	0.196
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.159
r_symmetry_nbd_refined	0.158
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.064
r_symmetry_xyhbond_nbd_other	0.046
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2266
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	100

Software

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