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Crystal structure of Fab F22-4 in complex with a Shigella flexneri 2a O-Ag pentadecasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C5S pdb entry 3C5S
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 2.61 52.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.86 α = 90 b = 137.15 β = 94.97 c = 109.38 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 45.74 99.2 0.112 0.112 5 3.8 179612 179612 -3 -3 16.86
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 97.5 0.668 0.668 1 3.5 25673
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 1.8 44.79 176903 176903 2670 99.11 0.1923 0.1923 0.19141 0.1989 0.25109 0.2545 RANDOM 18.781
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] -0.68 -0.02 2.2 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.102 r_dihedral_angle_4_deg 16.002 r_dihedral_angle_3_deg 14.173 r_dihedral_angle_1_deg 6.876 r_scangle_it 2.715 r_scbond_it 2.004 r_mcangle_it 1.957 r_angle_refined_deg 1.626 r_mcbond_it 1.578 r_angle_other_deg 0.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.102 r_dihedral_angle_4_deg 16.002 r_dihedral_angle_3_deg 14.173 r_dihedral_angle_1_deg 6.876 r_scangle_it 2.715 r_scbond_it 2.004 r_mcangle_it 1.957 r_angle_refined_deg 1.626 r_mcbond_it 1.578 r_angle_other_deg 0.804 r_mcbond_other 0.322 r_symmetry_hbond_refined 0.28 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.198 r_nbd_other 0.196 r_symmetry_vdw_other 0.196 r_nbtor_refined 0.181 r_symmetry_hbond_other 0.151 r_chiral_restr 0.091 r_nbtor_other 0.087 r_xyhbond_nbd_other 0.018 r_bond_refined_d 0.014 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 13125 Nucleic Acid Atoms Solvent Atoms 2124 Heterogen Atoms 481
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction SCALA data scaling PHASER phasing