9F19 | pdb_00009f19

Human USP30 chimera in complex with NK036 inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		Custom model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	76 mM NaOH, 100 mM Bicine, 10.2% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM L-Proline (Crystal 1)
2	VAPOR DIFFUSION, SITTING DROP		293	85 mM NaOH, 100 mM Bicine, 10.2% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM L-Proline (Crystal 2)
3	VAPOR DIFFUSION, SITTING DROP		293	88 mM NaOH, 100 mM Bicine, 11% (w/v) PEG 20,000, 1% (v/v) Dioxane, 10 mM Sarcosine (Crystal 3)

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.833	α = 90
b = 73.835	β = 90
c = 201.053	γ = 90

Symmetry
Space Group	P 21 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	3	x-ray	100	PIXEL	DECTRIS EIGER X 4M		2023-11-16	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	2.75	59.52	91.9	0.166	0.998	9.6	13.9		15438			78.31

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	2.75	3.23	69		1.536	0.73	1.9	13.9

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	2.75	59.51	1.34	15432	1543	68.79	0.2229	0.2181	0.2224	0.2661	0.2689	79.2

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	17.6004
f_angle_d	1.0907
f_chiral_restr	0.0549
f_plane_restr	0.0093
f_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3791
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	72

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.