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Crystal structure of phage derived Fab BdF1 with human Death Receptor 5 (DR5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D0G Chain S from 1d0g Chain AB from 1FVE experimental model PDB 1FVE Chain S from 1d0g Chain AB from 1FVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 Crystals from drops containing an equal volume of protein and well solution consisting of 20% PEG 3350, 0.2M Na2HPO4, 0.1 M Bis-Tris, pH 6.1-6.8. The crystals were cryo-protected with well solution supplemented with 20% PEG 200., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.814 α = 90 b = 61.389 β = 101.17 c = 108.269 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 ADSC QUANTUM 210 2003-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.00 ALS 8.2.1
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 2.3 50 97.1 0.089 6.7 3.4 54784 54784 -3 -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 2.3 2.38 97.3 0.419 2 3.8 5470
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 Chain S from 1d0g
Chain AB from 1FVE 2.32 30 -3 54443 48957 5486 97 0.2338 0.2338 0.22846 0.2318 0.28164 0.2825 RANDOM 12.83
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] 0.47 0.66 -1.09 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.303 r_dihedral_angle_4_deg 18.841 r_dihedral_angle_3_deg 17.824 r_dihedral_angle_1_deg 6.57 r_scangle_it 3.45 r_mcangle_it 3.326 r_mcbond_it 2.47 r_scbond_it 2.413 r_angle_refined_deg 1.3 r_angle_other_deg 0.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.303 r_dihedral_angle_4_deg 18.841 r_dihedral_angle_3_deg 17.824 r_dihedral_angle_1_deg 6.57 r_scangle_it 3.45 r_mcangle_it 3.326 r_mcbond_it 2.47 r_scbond_it 2.413 r_angle_refined_deg 1.3 r_angle_other_deg 0.766 r_mcbond_other 0.515 r_nbd_refined 0.192 r_symmetry_vdw_other 0.19 r_nbd_other 0.181 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.16 r_symmetry_vdw_refined 0.118 r_nbtor_other 0.083 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7756 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling AMoRE phasing