6EQS | pdb_00006eqs

Human Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RIY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	30% PEG3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, 5% 1,3-butandiol

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.326	α = 97.39
b = 55.969	β = 99.29
c = 123.034	γ = 90.52

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 PILATUS 2M-F		2016-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000030	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.32	43.77	91.5	0.059	0.999	6.8	2		227669

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.32	1.4	88.1		0.959	0.723	1.1	1.9

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3RIY	1.32	43.77	224952	2388	91.87	0.16076	0.16025	0.16	0.20856	0.2	RANDOM	21.373

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]
-2.34	3.38	-2.91	-1.76	0.81	4.1

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	47.72
r_dihedral_angle_2_deg	34.612
r_dihedral_angle_4_deg	20.43
r_sphericity_bonded	19.296
r_dihedral_angle_3_deg	13.724
r_long_range_B_refined	9.451
r_long_range_B_other	9.451
r_mcangle_it	8.762
r_mcangle_other	8.762
r_scangle_other	7.766
r_mcbond_it	7.279
r_mcbond_other	7.278
r_scbond_it	7.102
r_scbond_other	7.101
r_rigid_bond_restr	6.781
r_dihedral_angle_1_deg	6.418
r_angle_refined_deg	2.886
r_angle_other_deg	1.801
r_chiral_restr	0.276
r_bond_refined_d	0.031
r_gen_planes_refined	0.017
r_gen_planes_other	0.01
r_bond_other_d	0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8313
Nucleic Acid Atoms
Solvent Atoms	1086
Heterogen Atoms	440

Software

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