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Structure of anti-amyloid-beta Fab WO2 (Form A, P212121)
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 6.7 293 100mM MES, 10mM ZnSO4, 20% (v/v)PEG 550 monoethylether, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 56.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.447 α = 90 b = 90.496 β = 90 c = 123.279 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 CCD MAR CCD 165 mm bent conical Si-mirror (Rh coating); bent cylindrical Ge(111) monochromator 2004-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
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 1.6 19.94 98 0.101 16.6 4.8 76778 76623
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) 1.598 1.64 88.08 0.101 16.6 4.8 5010
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 (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 THROUGHOUT PDB entry 1PLG 1.6 19.9 69155 68579 7623 97.98 0.22 0.205 0.203 0.2115 0.226 0.2092 RANDOM 15.181
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.136 r_dihedral_angle_4_deg 18.114 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_1_deg 6.505 r_scangle_it 3.701 r_scbond_it 2.453 r_symmetry_metal_ion_refined 1.607 r_mcangle_it 1.572 r_angle_refined_deg 1.476 r_angle_other_deg 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.136 r_dihedral_angle_4_deg 18.114 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_1_deg 6.505 r_scangle_it 3.701 r_scbond_it 2.453 r_symmetry_metal_ion_refined 1.607 r_mcangle_it 1.572 r_angle_refined_deg 1.476 r_angle_other_deg 0.886 r_mcbond_it 0.811 r_symmetry_vdw_refined 0.505 r_metal_ion_refined 0.359 r_symmetry_vdw_other 0.312 r_nbd_refined 0.214 r_mcbond_other 0.207 r_nbd_other 0.203 r_symmetry_hbond_refined 0.185 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.093 r_nbtor_other 0.087 r_xyhbond_nbd_other 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3415 Nucleic Acid Atoms Solvent Atoms 482 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing