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Structure of urokinase receptor, urokinase and vitronectin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FD6 PDB ENTRY 2fd6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7.5 295 8% PEG 4000, 2.5% ethanol, 0.05% sodium azide, 50mM cacodylate pH 6.5, pH 7.5, MICRODIALYSIS, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.88 57.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.096 α = 90 b = 87.205 β = 94.31 c = 124.274 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 100 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 210 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.0 APS 24-ID-C 2 SYNCHROTRON NSLS BEAMLINE X12C 1.0 NSLS X12C
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 2.5 50 99.2 0.077 0.077 24.1 5.3 38381 42.2
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) 1,2 2.5 2.59 96 0.356 0.356 2.8 4.1 3675
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 2fd6 2.5 42.88 37032 1191 99.16 0.22993 0.22862 0.2322 0.2717 0.2722 RANDOM 62.232
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 -0.7 1.5 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.001 r_dihedral_angle_4_deg 19.28 r_dihedral_angle_3_deg 18.315 r_dihedral_angle_1_deg 7.848 r_scangle_it 2.926 r_scbond_it 2.001 r_angle_refined_deg 1.74 r_mcangle_it 1.264 r_angle_other_deg 1.11 r_mcbond_it 1.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.001 r_dihedral_angle_4_deg 19.28 r_dihedral_angle_3_deg 18.315 r_dihedral_angle_1_deg 7.848 r_scangle_it 2.926 r_scbond_it 2.001 r_angle_refined_deg 1.74 r_mcangle_it 1.264 r_angle_other_deg 1.11 r_mcbond_it 1.039 r_xyhbond_nbd_other 0.417 r_xyhbond_nbd_refined 0.236 r_nbd_refined 0.227 r_nbd_other 0.213 r_symmetry_vdw_other 0.184 r_nbtor_refined 0.182 r_mcbond_other 0.166 r_symmetry_vdw_refined 0.135 r_chiral_restr 0.122 r_symmetry_hbond_refined 0.121 r_nbtor_other 0.096 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6527 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing