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Crystal structure the Fab fragment of therapeutic antibody daclizumab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GIZ PDB ENTRY 3GIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M HEPES, 0.1M ammonium sulfate, 2% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 52.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.866 α = 90 b = 67.866 β = 90 c = 205.607 γ = 90
Symmetry Space Group P 41 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 IMAGE PLATE RIGAKU RAXIS IV 2008-12-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.6 20 98.3 0.14 3.8 11.4 15582
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 2.6 2.69 98.3 0.341 1.9 10.7 1490
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 3GIZ 2.6 20 15305 777 98.22 0.227 0.225 0.2377 0.275 0.2459 RANDOM 48.78
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] -0.82 -0.82 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.558 r_dihedral_angle_4_deg 22.388 r_dihedral_angle_3_deg 18.208 r_dihedral_angle_1_deg 6.351 r_scangle_it 3.202 r_scbond_it 2.258 r_mcangle_it 2.21 r_rigid_bond_restr 2.138 r_sphericity_free 1.993 r_mcbond_it 1.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.558 r_dihedral_angle_4_deg 22.388 r_dihedral_angle_3_deg 18.208 r_dihedral_angle_1_deg 6.351 r_scangle_it 3.202 r_scbond_it 2.258 r_mcangle_it 2.21 r_rigid_bond_restr 2.138 r_sphericity_free 1.993 r_mcbond_it 1.299 r_angle_refined_deg 1.242 r_sphericity_bonded 0.877 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.081 r_symmetry_hbond_refined 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3203 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CrystalClear data scaling CNS phasing