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Crystal structure of Fab F22-4 in complex with a Shigella flexneri 2a O-Ag decasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C5S PDB ENTRY 3c5s; chains C and D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 290 25% PEG 5000 MMe, 0.2M Li2SO4, 0.1M Tris, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.64 53.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.06 α = 90 b = 137.6 β = 95.15 c = 109.8 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 4 bent mirror 2006-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.8 47.946 99.7 0.105 0.105 5.5 3.8 182390 182390 -3 -3 18.8
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 1.8 1.9 99.4 0.622 0.622 1.1 3.7 26443
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3c5s; chains C and D 1.8 47.92 182354 182354 2708 99.67 0.177 0.177 0.176 0.1855 0.23 0.2354 RANDOM 19.808
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] -0.38 -0.22 1.62 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.794 r_dihedral_angle_4_deg 15.54 r_dihedral_angle_3_deg 13.052 r_dihedral_angle_1_deg 6.594 r_scangle_it 2.566 r_mcangle_it 2.001 r_scbond_it 1.905 r_angle_refined_deg 1.483 r_mcbond_it 1.358 r_angle_other_deg 0.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.794 r_dihedral_angle_4_deg 15.54 r_dihedral_angle_3_deg 13.052 r_dihedral_angle_1_deg 6.594 r_scangle_it 2.566 r_mcangle_it 2.001 r_scbond_it 1.905 r_angle_refined_deg 1.483 r_mcbond_it 1.358 r_angle_other_deg 0.778 r_mcbond_other 0.29 r_symmetry_hbond_refined 0.225 r_nbd_refined 0.192 r_nbd_other 0.185 r_nbtor_refined 0.177 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_other 0.177 r_xyhbond_nbd_refined 0.169 r_symmetry_vdw_other 0.154 r_chiral_restr 0.086 r_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13121 Nucleic Acid Atoms Solvent Atoms 2475 Heterogen Atoms 449
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction SCALA data scaling PHASER phasing