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The catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody Nb7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LHR 5LHR and 4JVP experimental model PDB 4JVP 5LHR and 4JVP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 288 100 mM HEPES, 1.6 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 3.59 65.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.67 α = 90 b = 94.67 β = 90 c = 121.57 γ = 120
Symmetry Space Group P 31 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 MAR CCD 165 mm 2014-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.04 MAX II I911-2
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 2.55 19.67 99.7 0.095 20.49 10.3 20993
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 2.55 2.64 1.046
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5LHR and 4JVP 2.55 19.67 1.36 20988 1049 99.96 0.1789 0.1767 0.1888 0.2191 0.2231
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 13.421 f_angle_d 0.686 f_chiral_restr 0.027 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2856 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing