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Crystal Structure of a Michaelis Complex between Plasminogen Activator Inhibitor-1 and Urokinase-type Plasminogen Activator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DVM PDB ENTRY 1DVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 1.4M ammonium sulfate, 0.1M Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.33 63.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.711 α = 90 b = 97.711 β = 90 c = 171.916 γ = 120
Symmetry Space Group P 32 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 DIFFRACTOMETER 2010-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0 SSRF BL17U
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 2.3 99 99.9 0.162 0.185 21.5 5.9 81438 80462
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.34 98.5 0.589 0.633 3.4 4.2 3996
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DVM 2.3 38.32 40338 2142 99.11 0.22304 0.22049 0.2171 0.27199 0.2694 RANDOM 28.466
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 r_dihedral_angle_2_deg 34.977 r_dihedral_angle_4_deg 19.617 r_dihedral_angle_3_deg 17.958 r_dihedral_angle_1_deg 6.72 r_scangle_it 2.72 r_scbond_it 1.562 r_angle_refined_deg 1.26 r_mcangle_it 1.14 r_mcbond_it 0.586 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.977 r_dihedral_angle_4_deg 19.617 r_dihedral_angle_3_deg 17.958 r_dihedral_angle_1_deg 6.72 r_scangle_it 2.72 r_scbond_it 1.562 r_angle_refined_deg 1.26 r_mcangle_it 1.14 r_mcbond_it 0.586 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4926 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 10
Software Software Software Name Purpose HKL-2000 data collection CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing