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Fab fragment of 3D6 in complex with amyloid beta 1-40
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 3D6 Fab antibody model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 2.5 M NaCl, 0.1 Imidazole pH 8.0, 0.2 ZnAc2., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.85 56.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.04 α = 90 b = 84.94 β = 90 c = 175.69 γ = 90
Symmetry Space Group P 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 MAR 2008-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 87.845 100 0.059 0.059 19.9 5.8 31474 22.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 100 0.189 0.189 3.8 5.9 2272
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3D6 FAB ANTIBODY 2.2 76.474 31429 1584 99.97 0.18 0.177 0.1782 0.227 0.2253 29.38
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.428 f_angle_d 1.181 f_chiral_restr 0.08 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3301 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 53
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction Blu-Ice data collection COMO phasing