9VGE | pdb_00009vge

SIRT2 demyristoylation intermediate I structure

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% PEG 2000MME

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.059	α = 90
b = 77.646	β = 97.988
c = 55.955	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		2024-10-29	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	2.56	55.474	94.4	0.994	11.4	5.1		9655

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	2.56	2.67			0.491

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	2.56	55.474	9638	521	94.37	0.207	0.2029	0.212	0.2819	0.2987	55.879

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]
7.082		3.682	-3.976		-3.983

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.035
r_dihedral_angle_2_deg	15.54
r_dihedral_angle_6_deg	13.301
r_lrange_it	8.57
r_lrange_other	8.57
r_dihedral_angle_1_deg	6.849
r_scangle_it	5.262
r_scangle_other	5.261
r_mcangle_it	5.088
r_mcangle_other	5.086
r_mcbond_it	3.407
r_mcbond_other	3.401
r_scbond_it	3.309
r_scbond_other	3.308
r_angle_refined_deg	1.628
r_dihedral_angle_other_2_deg	1.488
r_angle_other_deg	0.515
r_symmetry_xyhbond_nbd_refined	0.296
r_nbd_other	0.238
r_symmetry_nbd_refined	0.229
r_symmetry_nbd_other	0.221
r_nbd_refined	0.218
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.156
r_metal_ion_refined	0.155
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.069
r_bond_refined_d	0.027
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2297
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	66

Software

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