7FQH | pdb_00007fqh

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	26mg/mL deglycosylated 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 22.5% PEG smear low, 0.1M MES/NaOH, 10% v/v 2-Propanol, total volume 200nL

Crystal Properties
Matthews coefficient	Solvent content
1.4	11.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.798	α = 90
b = 117.798	β = 90
c = 102.812	γ = 120

Symmetry
Space Group	P 3 2 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	CCD	MARMOSAIC 225 mm CCD		2020-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00005	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	2.18	51.41	100	0.244	0.257	0.997	7.7	10.302		43660			51.649

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.18	2.23	100		4.495	4.725	0.219	0.52	10.565

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	inhouse model	2.18	51.46	27034	1396	65.09	0.2258	0.2234	0.22	0.2724	0.27	RANDOM	38.796

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]
0.25	0.13		0.25		-0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.437
r_dihedral_angle_4_deg	18.667
r_dihedral_angle_3_deg	15.005
r_dihedral_angle_1_deg	7.011
r_mcangle_it	1.529
r_angle_refined_deg	1.377
r_angle_other_deg	1.202
r_mcbond_it	0.835
r_mcbond_other	0.835
r_chiral_restr	0.058

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.437
r_dihedral_angle_4_deg	18.667
r_dihedral_angle_3_deg	15.005
r_dihedral_angle_1_deg	7.011
r_mcangle_it	1.529
r_angle_refined_deg	1.377
r_angle_other_deg	1.202
r_mcbond_it	0.835
r_mcbond_other	0.835
r_chiral_restr	0.058
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6279
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	2963

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.