Experiment: 9F6G

Human USP30 chimera bound to Ubiquitin-PA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		custom sequence
experimental model	PDB	1UBQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.56 M sodium citrate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.639	α = 90
b = 50.706	β = 90
c = 156.56	γ = 90

Symmetry
Space Group	P 21 21 21

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 4M		2024-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.5	46.64	97.1	0.073	0.998	10.7	6.2		58606			19.81

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	96.8		1.24	0.426	1.4	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	44.7	1.34	58467	2888	96.73	0.1843	0.183	0.183	0.2107	0.2106	29.02

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.2624
f_angle_d	1.3305
f_chiral_restr	0.0885
f_bond_d	0.0141
f_plane_restr	0.0126

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2767
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	4

Software

Software
Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
xia2	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building