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Crystal Structure of monoclonal Fab F22-4 specific for Shigella flexneri 2a O-Ag
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EJO VL/VH dimer: pdb entry 1ejo residues 2002L-2109L; pdb entry 1aj4 residues 1H-99H; CL/CH dimer: pdb entry 1f11 residues 108A-211A and 114B-227B. experimental model PDB 1AJ4 VL/VH dimer: pdb entry 1ejo residues 2002L-2109L; pdb entry 1aj4 residues 1H-99H; CL/CH dimer: pdb entry 1f11 residues 108A-211A and 114B-227B. experimental model PDB 1F11 VL/VH dimer: pdb entry 1ejo residues 2002L-2109L; pdb entry 1aj4 residues 1H-99H; CL/CH dimer: pdb entry 1f11 residues 108A-211A and 114B-227B.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 290 24% PEG 2000 MME, 190mM MgCl2, 50mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.12 41.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.26 α = 77.53 b = 59.83 β = 83.97 c = 74.38 γ = 80.89
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MAR CCD 165 mm bent mirror 2001-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 72.36 95.8 0.068 0.068 7 3.8 50673 50673 -3
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) 2 2.11 94.8 0.144 0.144 5.1 3.3 7292
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT VL/VH dimer: pdb entry 1ejo residues 2002L-2109L; pdb entry 1aj4 residues 1H-99H; CL/CH dimer: pdb entry 1f11 residues 108A-211A and 114B-227B. 2 72.36 50671 50671 1307 95.76 0.201 0.201 0.199 0.26 0.2862 RANDOM 28.559
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] 0.75 1.93 -1.83 -0.4 -0.88 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.887 r_dihedral_angle_3_deg 14.807 r_dihedral_angle_4_deg 14.261 r_dihedral_angle_1_deg 6.54 r_scangle_it 2.397 r_mcangle_it 2.123 r_scbond_it 1.781 r_angle_refined_deg 1.484 r_mcbond_it 1.393 r_angle_other_deg 0.783
Show All KeysRMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.887 r_dihedral_angle_3_deg 14.807 r_dihedral_angle_4_deg 14.261 r_dihedral_angle_1_deg 6.54 r_scangle_it 2.397 r_mcangle_it 2.123 r_scbond_it 1.781 r_angle_refined_deg 1.484 r_mcbond_it 1.393 r_angle_other_deg 0.783 r_mcbond_other 0.268 r_symmetry_hbond_refined 0.256 r_symmetry_vdw_other 0.248 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.188 r_nbd_other 0.186 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.154 r_nbtor_other 0.087 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Hide All KeysNon-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6482 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction SCALA data scaling AMoRE phasing