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STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 LMW human uPA/A145 was concentrated to 10 mg/ml
and incubated in 50 mM HEPES, 5.0 mM NaCl. pH 7.0,
5.0 mM benzamidne for 15 min on ice. The complex was
crystallized by vapor diffusion in hanging drops containing
equal volumes of protein-inhibitor solution (0.28 mM uPA/A145,
1.4 mM inhibitor) and well solution (20 % 2-propanol,
20 % PEG 4K, 100 mM sodium citrate, pH 6.5) sealed over the well.
Crystal Properties Matthews coefficient Solvent content 1.99 25.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.78 α = 90 b = 49.05 β = 113.68 c = 66.85 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 298 IMAGE PLATE RIGAKU RAXIS IV++ MSC MIRRORS 1999-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1
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 1.48 38.25 64 0.093 4.5 1.8 16139 1
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) 1.85 1.93 31 0.21 2
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) Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER PLUS REFINEMENT X-PLOR PDB1LMW 1.85 7.5 1.9 13200 1343 63.7 0.185 0.185 0.1964 0.237
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 x_dihedral_angle_d 24.4 x_angle_deg 4 x_improper_angle_d 0.41 x_bond_d 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4075 Nucleic Acid Atoms Solvent Atoms 1152 Heterogen Atoms 72
Software Software Software Name Purpose bioteX data collection bioteX data reduction X-PLOR model building Quanta model building Insight II model building X-PLOR refinement bioteX data scaling X-PLOR phasing