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Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8FAB PDB ENTRY 8FAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 Protein (7mg/mL in 20 mM Tris-HCl, 150 mM NaCl) was mixed with equal volume of well solution (30% PEG 4K, 0.1 M Tris-HCl pH 8.5, 0.2M MgCl2), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.74 55.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.317 α = 90 b = 128.317 β = 90 c = 68.386 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 ADSC QUANTUM 315 2004-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.2 50 98.9 0.087 18.2 8.3 10908 10792 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.39 96.8 0.305 5.7 8.3 1741
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 8FAB 3.2 30 10792 10792 1060 97.56 0.24763 0.24763 0.24115 0.2405 0.30463 0.2985 RANDOM 111.762
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] -8.75 -4.37 -8.75 13.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.41 r_dihedral_angle_4_deg 20.816 r_dihedral_angle_3_deg 19.052 r_dihedral_angle_1_deg 6.087 r_angle_refined_deg 1.226 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3896 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling