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Crystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with IL-2Ra (CD25) ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NFS PDB ENTRY 3NFS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M Tris-HCl, 0.2M MgCl2, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.167 α = 90 b = 114.973 β = 90 c = 247.555 γ = 90
Symmetry Space Group C 2 2 21
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 RAYONIX MX225HE 2009-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9796 SSRF BL17U
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 2.8 50 95.5 0.158 7.1 4.6 31671
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 2.8 2.9 99.8 0.384 2.9 3.9
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 3NFS 2.86 50 31669 1599 93.08 0.255 0.253 0.2487 0.301 0.2494 RANDOM 69.528
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] 1.41 -2.44 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.654 r_dihedral_angle_3_deg 15.662 r_dihedral_angle_4_deg 13.085 r_mcangle_it 4.92 r_dihedral_angle_1_deg 4.889 r_scangle_it 4.827 r_rigid_bond_restr 4.542 r_scbond_it 3.902 r_mcbond_it 3.146 r_sphericity_bonded 1.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.654 r_dihedral_angle_3_deg 15.662 r_dihedral_angle_4_deg 13.085 r_mcangle_it 4.92 r_dihedral_angle_1_deg 4.889 r_scangle_it 4.827 r_rigid_bond_restr 4.542 r_scbond_it 3.902 r_mcbond_it 3.146 r_sphericity_bonded 1.559 r_sphericity_free 1.457 r_angle_refined_deg 1.052 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8324 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing