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Crystal structure of a conformation-dependent rabbit IgG Fab specific for amyloid prefibrillar oligomers
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.2 M Magnesium sulfate 20 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.934 α = 90 b = 42.184 β = 114.93 c = 86.179 γ = 90
Symmetry Space Group C 1 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 ADSC QUANTUM 315r 2007-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979462 SSRL BL9-1
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 1.54 31.01 87.6 0.081 10.2 6.46 56536
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 1.54 1.6 49.7 0.53 2 4.67 3191
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.54 31 56401 2857 87.35 0.2004 0.1973 0.1922 0.2592 0.2549 RANDOM 27.7234
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] -1.22 -1.19 2.11 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.487 r_sphericity_free 28.311 r_dihedral_angle_3_deg 12.169 r_dihedral_angle_4_deg 11.081 r_sphericity_bonded 10.391 r_dihedral_angle_1_deg 6.666 r_rigid_bond_restr 2.655 r_angle_refined_deg 1.507 r_chiral_restr 0.092 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.487 r_sphericity_free 28.311 r_dihedral_angle_3_deg 12.169 r_dihedral_angle_4_deg 11.081 r_sphericity_bonded 10.391 r_dihedral_angle_1_deg 6.666 r_rigid_bond_restr 2.655 r_angle_refined_deg 1.507 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3152 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 5
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction