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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 12% PEG 3350, 50mM HEPES pH 7.5, MICRODIALYSIS, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.75 55.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.353 α = 90 b = 105.187 β = 90 c = 55.36 γ = 90
Symmetry Space Group P 21 21 2
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 MARMOSAIC 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0 APS 23-ID-B
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 2.8 100 99.5 0.081 0.081 33.1 5.9 14540 82
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 2.8 2.9 100 0.803 0.803 2.6 5.9
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 2.8 27.68 13778 726 99.6 0.244 0.241 0.3048 0.308 0.3328 RANDOM 54.32
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] 0.48 -3.25 2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.371 r_dihedral_angle_3_deg 21.248 r_dihedral_angle_4_deg 19.56 r_dihedral_angle_1_deg 9.464 r_scangle_it 2.154 r_angle_refined_deg 1.821 r_scbond_it 1.356 r_angle_other_deg 1.048 r_mcangle_it 0.958 r_mcbond_it 0.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.371 r_dihedral_angle_3_deg 21.248 r_dihedral_angle_4_deg 19.56 r_dihedral_angle_1_deg 9.464 r_scangle_it 2.154 r_angle_refined_deg 1.821 r_scbond_it 1.356 r_angle_other_deg 1.048 r_mcangle_it 0.958 r_mcbond_it 0.746 r_nbd_refined 0.266 r_symmetry_vdw_other 0.246 r_nbd_other 0.221 r_xyhbond_nbd_refined 0.196 r_nbtor_refined 0.191 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_other 0.163 r_mcbond_other 0.105 r_chiral_restr 0.102 r_nbtor_other 0.1 r_symmetry_hbond_refined 0.064 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3394 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing