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P22 Tailspike complexed with S.Paratyphi O antigen octasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VFM ENSEMBLE OF PDB ENTRIES 2VFM, 2VFN, and 2VFQ experimental model PDB 2VFN ENSEMBLE OF PDB ENTRIES 2VFM, 2VFN, and 2VFQ experimental model PDB 2VFQ ENSEMBLE OF PDB ENTRIES 2VFM, 2VFN, and 2VFQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 277.15 1.5 Ammonium sulfate, 0.1M sodium phosphate over reservoir 1.0 Ammonium sulfate, 0.1M sodium phosphate, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K 2 MICRODIALYSIS 7.5 293.15 addition of 2mM S.Paratyphi o antigen octasaccharide in 0.1M Tris, 1M sodium phosphate, pH 7.5, MICRODIALYSIS, temperature 293.15K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.943 α = 90 b = 119.943 β = 90 c = 119.943 γ = 90
Symmetry Space Group P 21 3
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 RAYONIX MX-225 mirrors,
double crystal monochromator,
MD2 microdiffractometer,
MK3-minikappa 2010-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 1.75 33.27 99.9 0.133 16.1 5.7 58030 11.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 99.9 3.2 5.2 4247
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 ENSEMBLE OF PDB ENTRIES 2VFM, 2VFN, and 2VFQ 1.75 33.27 55128 2902 99.91 0.13682 0.13578 0.1344 0.15588 0.1502 RANDOM 10.308
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 35.937 r_dihedral_angle_3_deg 11.173 r_dihedral_angle_4_deg 9.842 r_dihedral_angle_1_deg 6.671 r_scangle_it 2.814 r_scbond_it 1.719 r_angle_refined_deg 1.372 r_mcangle_it 1.028 r_angle_other_deg 0.831 r_mcbond_it 0.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.937 r_dihedral_angle_3_deg 11.173 r_dihedral_angle_4_deg 9.842 r_dihedral_angle_1_deg 6.671 r_scangle_it 2.814 r_scbond_it 1.719 r_angle_refined_deg 1.372 r_mcangle_it 1.028 r_angle_other_deg 0.831 r_mcbond_it 0.566 r_mcbond_other 0.153 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 4182 Nucleic Acid Atoms Solvent Atoms 660 Heterogen Atoms 101
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling