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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 7.4, 1.4 mM
4-iodobenzo[b]thiophene-2-carboxamidine 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 2.01 25.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.09 α = 90 b = 49.78 β = 113.29 c = 66.65 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 1998-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 1.32 38.49 68 0.088 4 2.8 27491 0.8
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) 1.75 1.83 38.9 0.235 1.6
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 1.75 7.5 2 16929 1709 68 0.195 0.195 0.1978 0.244
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 0.43 x_bond_d 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4188 Nucleic Acid Atoms Solvent Atoms 1152 Heterogen Atoms 81
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