Experiment: 8EDE

Crystal structure of covalent inhibitor 2-chloro-N'-(N-(4-chlorophenyl)-N-methylglycyl)acetohydrazide bound to Ubiquitin C-terminal Hydrolase-L1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ETL	2ETL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294.15	0.1M tri-Sodium citrate 2.4M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.35	48.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.003	α = 90
b = 110.003	β = 90
c = 79.609	γ = 90

Symmetry
Space Group	P 4 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 PILATUS 6M		2022-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.98	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.799	50	100	0.147	0.153	0.043	5.8	12.7		45890			30.49

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	100		2.229	2.322	0.647	0.617		12.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	THROUGHOUT	2ETL	1.799	45.252	1.34	45838	2371	99.92	0.1946	0.1928	0.1938	0.2267	0.2265	47.1589

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	15.537
f_angle_d	0.834
f_chiral_restr	0.058
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3386
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	80

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
HKL-3000	data reduction