8Q00 | pdb_00008q00

TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		apo-TssM; individual search models for Ig-like and catalytic domain; Ig-like domain had its b1 strand removed

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
3.06	49.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.75	α = 90
b = 103.75	β = 90
c = 191.52	γ = 90

Symmetry
Space Group	P 41 21 2

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 EIGER X 16M	default	2021-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.62	103.74	99.9	0.076	0.08	0.9990000000000001	18.54	13.42		132701

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.62	1.66			2.335	2.425	0.516	1.19

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.62	91.22	130701	2000	99.95	0.17473	0.17436	0.1846	0.19822	0.2035	RANDOM	28.719

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]
0.47			0.47		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.039
r_dihedral_angle_2_deg	10.686
r_long_range_B_refined	8.062
r_long_range_B_other	8.013
r_scangle_other	6.612
r_dihedral_angle_1_deg	6.267
r_scbond_it	4.536
r_scbond_other	4.536
r_mcangle_it	3.787
r_mcangle_other	3.787
r_mcbond_it	2.789
r_mcbond_other	2.789
r_angle_refined_deg	1.76
r_angle_other_deg	0.579
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5704
Nucleic Acid Atoms
Solvent Atoms	724
Heterogen Atoms	23

Software

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