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Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and an anti-upar antibody at 1.9 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FAT PDB ENTRY 2FAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 6.5 298 4% PEG4000, 5% ethylene glycol, 5% methanol, 0.05% sodium azide, 50 mM cacodylate, pH 6.5, MICRODIALYSIS, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.07 59.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.792 α = 90 b = 86.805 β = 94.54 c = 124.69 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MARRESEARCH 2005-04-09 M SINGLE WAVELENGTH 2 1 CCD 3 1 CCD 4 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID 2 SYNCHROTRON NSLS BEAMLINE X25 1.00 NSLS X25 3 SYNCHROTRON NSLS BEAMLINE X12C 1.0 NSLS X12C 4 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 1.85 41.36 94.5 0.064 16.1 86852 21
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 1.85 2.08 77.5 0.338 1.97
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2FAT 1.9 41.36 86852 83101 4228 95.8 0.239 0.239 0.239 0.2407 0.276 RANDOM 32.9
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] -0.31 -3.7 4.95 -4.64
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.2 c_angle_deg 1.5 c_improper_angle_d 0.9 c_bond_d 0.007 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6139 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 125
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing