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The crystal structure of the YSd1 Fab bound to DR5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FVE 1FVE variants
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 292 20% PEG 8000, 0.2M MgAcetate, 0.1M NaCacodylate pH 6.2-6.6, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.4 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.059 α = 90 b = 147.059 β = 90 c = 144.947 γ = 120
Symmetry Space Group P 32 2 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 CUSTOM-MADE 2004-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.92086 APS 19-BM
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 3.35 50 99.7 0.124 8.3 5.6 26539 26539 -3 42
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 3.35 3.47 99.8 0.338 4.2 5.7 2582
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 1FVE variants 3.35 30 -3 26539 26003 2603 98.34 0.22975 0.22975 0.22408 0.2094 0.28028 0.2533 RANDOM 21.287
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] -1.2 -0.6 -1.2 1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.48 r_scangle_it 3.932 r_mcangle_it 3.666 r_scbond_it 2.491 r_mcbond_it 2.152 r_angle_refined_deg 1.339 r_angle_other_deg 0.899 r_symmetry_hbond_refined 0.275 r_symmetry_vdw_other 0.25 r_nbd_other 0.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.48 r_scangle_it 3.932 r_mcangle_it 3.666 r_scbond_it 2.491 r_mcbond_it 2.152 r_angle_refined_deg 1.339 r_angle_other_deg 0.899 r_symmetry_hbond_refined 0.275 r_symmetry_vdw_other 0.25 r_nbd_other 0.226 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.207 r_xyhbond_nbd_refined 0.17 r_nbtor_other 0.088 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8149 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing