8Q4B

Endothiapepsin in complex with ligand (3R,5R)-3-(2-((methyl(prop-2-yn-1-yl)amino)methyl)thiazol-4-yl)-5-(3-(2-nitrophenyl)-1,2,4-oxadiazol-5-yl)pyrrolidin-3-ol (CBWS-SE-163.1)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Available inhouse structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	292	Protein at 5 mg/mL in 100 mM ammoniumacetate pH 4.6, reservoir: 100 mM ammoniumacetate, 100 mM sodium acetate pH 4.6, 24 % PEG4000, 292 K, 2+2 yL drops over 1 mL reservoir, streak seeding

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.755	α = 90
b = 72.882	β = 108.47
c = 51.785	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 X 16M		2022-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	0.688813	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.28	50	93.4	0.999	12.04	3.73		75363			15.73

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.28	1.36	92		0.615	1.09	3.68

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.28	36.68	1.35	75335	3766	93.51	0.1928	0.192	0.2071	22.84

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	12.5727
f_angle_d	0.7976
f_chiral_restr	0.0737
f_plane_restr	0.005
f_bond_d	0.0044

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2362
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	70

Software

Software
Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

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.