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Synthesis of a Weak Basic uPA Inhibitor and Crystal Structure of Complex with uPA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 2.0 M ammonium sulfate, 50 mM sodium citrate pH 4.6 and 5% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 42.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.916 α = 90 b = 120.916 β = 90 c = 42.875 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 2011-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.01 60.46 79.02 15581 12312
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.24 95.37 7.73 4.68
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.01 60.46 11690 620 79 0.211 0.207 0.214 0.285 0.2829 RANDOM 20.93
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] -0.13 -0.13 -0.13 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.736 r_dihedral_angle_3_deg 18.482 r_dihedral_angle_4_deg 16.445 r_dihedral_angle_1_deg 7.754 r_scangle_it 4.242 r_scbond_it 2.654 r_angle_refined_deg 2.01 r_mcangle_it 1.748 r_mcbond_it 0.969 r_angle_other_deg 0.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.736 r_dihedral_angle_3_deg 18.482 r_dihedral_angle_4_deg 16.445 r_dihedral_angle_1_deg 7.754 r_scangle_it 4.242 r_scbond_it 2.654 r_angle_refined_deg 2.01 r_mcangle_it 1.748 r_mcbond_it 0.969 r_angle_other_deg 0.922 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1952 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 27
Software Software Software Name Purpose PROTEUM PLUS data collection REFMAC refinement