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Crystal structure of human Urokinase-type plasminogen activator in complex with bicycle peptide inhibitor UK970
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QN7 3QN7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.3 293 7% PEG400, 50mM Citrato, 1.8 M (NH4)2SO4; 20% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.01 38.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.315 α = 90 b = 121.315 β = 90 c = 42.817 γ = 120
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 PILATUS3 X 2M 2021-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 1.8 39.68 99.9 0.14 15.4 7.9 21768
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 1.8 1.84 0.82
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 3QN7 1.8 39.68 20685 1082 99.9 0.209 0.208 0.2102 0.229 0.239 RANDOM 23.9
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] -0.44 -0.22 -0.44 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.633 r_dihedral_angle_4_deg 20.768 r_dihedral_angle_3_deg 14.544 r_dihedral_angle_1_deg 7.38 r_angle_refined_deg 1.655 r_chiral_restr 0.113 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.633 r_dihedral_angle_4_deg 20.768 r_dihedral_angle_3_deg 14.544 r_dihedral_angle_1_deg 7.38 r_angle_refined_deg 1.655 r_chiral_restr 0.113 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2065 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing