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Structure of anti-uPAR Fab ATN-658
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.25 295 20-22% PEG3350, 0.1M Tris(PH 8.0-8.5), vapor diffusion, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.313 α = 90 b = 132.296 β = 106.73 c = 46.831 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 2006-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-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 1.6 66.08 85.7 0.094 9.4 3 49312
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 1.6 1.66 70 0.29 2.6
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 2DDQ 1.6 50 49278 2511 85.6 0.201 0.198 0.2069 0.246 0.2523 RANDOM 28.91
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 2.44 -1.51 3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.675 r_dihedral_angle_4_deg 23.912 r_dihedral_angle_3_deg 12.615 r_dihedral_angle_1_deg 6.534 r_scangle_it 3.083 r_scbond_it 2.186 r_mcangle_it 1.481 r_angle_refined_deg 1.407 r_mcbond_it 0.927 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.675 r_dihedral_angle_4_deg 23.912 r_dihedral_angle_3_deg 12.615 r_dihedral_angle_1_deg 6.534 r_scangle_it 3.083 r_scbond_it 2.186 r_mcangle_it 1.481 r_angle_refined_deg 1.407 r_mcbond_it 0.927 r_nbtor_refined 0.302 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.133 r_symmetry_vdw_refined 0.12 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3303 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing