7FQK

Crystal Structure of human Legumain in complex with (2S)-N-[(3S)-5-amino-1-(1,3-oxazol-2-yl)-5-oxopent-1-yn-3-yl]-1-[1-[4-(trifluoromethoxy)phenyl]cyclopropanecarbonyl]pyrrolidine-2-carboxamide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	28.5mg/mL protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 20% v/v PEG smear broad, 0.1M MES/NaOH pH 6.5, total volume 200nL

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.489	α = 90
b = 102.489	β = 90
c = 330.991	γ = 90

Symmetry
Space Group	P 43 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	CCD	MARMOSAIC 225 mm CCD		2021-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99991	SLS	X10SA

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	1.97	87.13	99.8	0.531	0.552	0.996	4.82	13.59		125523			48.543

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.02	99.7		19.236	19.961	0.04	13.942

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	inhouse model	1.97	87.13	49711	2636	41.7	0.1959	0.194	0.2325	RANDOM	40.431

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]
-0.15			-0.15		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.174
r_dihedral_angle_4_deg	14.924
r_dihedral_angle_3_deg	14.546
r_dihedral_angle_1_deg	5.369
r_mcangle_it	2.162
r_angle_refined_deg	1.773
r_angle_other_deg	1.514
r_mcbond_it	1.268
r_mcbond_other	1.268
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.174
r_dihedral_angle_4_deg	14.924
r_dihedral_angle_3_deg	14.546
r_dihedral_angle_1_deg	5.369
r_mcangle_it	2.162
r_angle_refined_deg	1.773
r_angle_other_deg	1.514
r_mcbond_it	1.268
r_mcbond_other	1.268
r_chiral_restr	0.102
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_gen_planes_other	0.009
r_bond_other_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8414
Nucleic Acid Atoms
Solvent Atoms	537
Heterogen Atoms	4036

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	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.