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New Pharmacophore for Serine Protease Inhibition Revealed by Crystal Structure of Human Urokinase-type Plasminogen Activator Complexed with a Cyclic Peptidyl Inhibitor, upain-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F5K PDB ENTRY 1F5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 298 0.05M sodium citrate, 1.95M (NH4)2SO4, 0.05% NaN3, 5% PEG 400, pH 4.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 37.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.481 α = 90 b = 120.481 β = 90 c = 42.117 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 CCD BRUKER SMART 6000 2005-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.15 60.24 99.64 0.1233 0.1261 5.83 6.89 16947 2 2 11.1
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) 2.15 2.28 99.8 0.44 1.94 6.89
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1F5K 2.15 60.24 12396 1027 100 0.218 0.218 0.2349 0.261 RANDOM 24.4
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] -5.25 -0.92 -5.25 10.5
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.6 c_scangle_it 2.83 c_angle_deg 2.8 c_mcangle_it 2.34 c_improper_angle_d 2.04 c_scbond_it 1.98 c_mcbond_it 1.46 c_bond_d 0.014 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.6 c_scangle_it 2.83 c_angle_deg 2.8 c_mcangle_it 2.34 c_improper_angle_d 2.04 c_scbond_it 1.98 c_mcbond_it 1.46 c_bond_d 0.014 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2000 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PROTEUM PLUS data collection PROTEUM PLUS data reduction SCALEPACK data scaling CNS phasing