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Crystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PLG PDB ENTRY 1PLG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 295 100mM bicine, 200mM MgCl2, 20% w/v PEG 8000 , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.81 31.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.658 α = 90 b = 66.365 β = 90 c = 115.337 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS IV++ cappilary optics 2005-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.59 20.383 99.7 0.073 11.4 4.49 53416 53254
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) 1.593 1.634 100 0.03 3.8 3.02 3785
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 (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 1PLG 1.593 20.38 53416 50573 2681 99.7 0.20897 0.2068 0.2141 0.24968 0.2144 RANDOM 11.853
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 r_dihedral_angle_2_deg 30.227 r_dihedral_angle_4_deg 21.704 r_dihedral_angle_3_deg 13.392 r_dihedral_angle_1_deg 6.819 r_scangle_it 2.944 r_scbond_it 2.241 r_angle_refined_deg 1.553 r_mcangle_it 1.292 r_mcbond_it 1.068 r_angle_other_deg 0.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.227 r_dihedral_angle_4_deg 21.704 r_dihedral_angle_3_deg 13.392 r_dihedral_angle_1_deg 6.819 r_scangle_it 2.944 r_scbond_it 2.241 r_angle_refined_deg 1.553 r_mcangle_it 1.292 r_mcbond_it 1.068 r_angle_other_deg 0.931 r_symmetry_vdw_refined 0.326 r_symmetry_vdw_other 0.278 r_mcbond_other 0.233 r_nbd_other 0.209 r_symmetry_hbond_refined 0.203 r_nbd_refined 0.188 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.097 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3443 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction SCALA data scaling