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Structure of anti-uPAR Fab ATN-658 in complex with uPAR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BT2 3BT2(chain A, B, U), 4K23(chain H, L) experimental model PDB 4K23 3BT2(chain A, B, U), 4K23(chain H, L)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.1M HEPES pH 7.5, 55%(v/v) Tacsimate, 2%(v/v) 2-methyl-1,3-propanediol, vapor diffusion, sitting drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 5.1 75.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.659 α = 90 b = 164.659 β = 90 c = 391.582 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 MARMOSAIC 300 mm CCD 2007-01-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.04 NSLS X29A
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 4.5 27 99.7 0.139 7.9 4.4 12451
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 4.5 4.66 100 0.841 4.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3BT2(chain A, B, U), 4K23(chain H, L) 4.5 26.902 1.34 12432 602 99.28 0.22 0.2174 0.2246 0.2751 0.2248 284.9089
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] 13.44 13.44 -26.88
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.414 f_angle_d 2.017 f_chiral_restr 0.132 f_bond_d 0.013 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6690 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 81
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing