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Crystal Structure of human Legumain in complex with (2S)-N-[(1S)-3-amino-1-cyano-3-oxopropyl]-1-[1-[4-[(2,4-difluorophenyl)methoxy]phenyl]cyclopropanecarbonyl]pyrrolidine-2-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other INHOUSE MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 25.7mg/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 high, 0.15M Li2SO4, 0.05M MgCL2, 0.1M HEPES/NaOH pH 7.8, total volume 200nL
Crystal Properties Matthews coefficient Solvent content 2.01 38.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 229.393 α = 90 b = 66.57 β = 100.93 c = 79.108 γ = 90
Symmetry Space Group C 1 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 2021-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99982 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 112.62 99 0.076 8.32 3.02 128574 35.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 98.7 2.079 0.49 3
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 1.7 112.62 86420 4617 70.2 0.171 0.169 0.1792 0.201 0.209 RANDOM 20.92
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] -0.07 0.04 -0.03 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.719 r_dihedral_angle_3_deg 13.166 r_dihedral_angle_4_deg 10.449 r_dihedral_angle_1_deg 6.829 r_mcangle_it 1.891 r_angle_refined_deg 1.443 r_angle_other_deg 1.326 r_mcbond_it 1.24 r_mcbond_other 1.224 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.719 r_dihedral_angle_3_deg 13.166 r_dihedral_angle_4_deg 10.449 r_dihedral_angle_1_deg 6.829 r_mcangle_it 1.891 r_angle_refined_deg 1.443 r_angle_other_deg 1.326 r_mcbond_it 1.24 r_mcbond_other 1.224 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6341 Nucleic Acid Atoms Solvent Atoms 664 Heterogen Atoms 227
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing