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Matriptase in complex with the synthetic inhibitor (S)-3-(3-(4-(3-(tert-butyl)ureido)piperidin-1-yl)-2-((3'-fluoro-4'-(hydroxymethyl)-[1,1'-biphenyl])-3-sulfonamido)-3-oxopropyl)benzimidamide (MI-1904)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 100 mM Sodium acetate pH 4.6, 2 M Sodium formate, protein concentration 7 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.37 48.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.687 α = 90 b = 80.408 β = 95.71 c = 40.714 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 PIXEL DECTRIS PILATUS 6M 2018-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.68644987696 50 97.5 0.062 0.999 13.48 3.78 27322 18.9933085518
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.79 97.6 0.485 0.815 2.41 3.82
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 2GV6 1.69 40.5119860988 1.35315402303 27021 1352 97.4853885562 0.171933711265 0.170323632146 0.1739 0.201903857021 0.2029 25.5897796376
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 13.7720156604 f_angle_d 1.01311868117 f_chiral_restr 0.0669269745891 f_bond_d 0.00936450644835 f_plane_restr 0.00786004161302
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1828 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 47
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing Coot model building