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Fab Structure of lipid A-specific antibody S1-15 in complex with lipid A carbohydrate backbone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ODS PDB ENTRY 4ODS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 289 0.1M NaCl, 0.1M Bicine, and 30% (w/v) PEG 550 MME, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.44 49.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.471 α = 90 b = 77.471 β = 90 c = 156.205 γ = 90
Symmetry Space Group P 43 21 2
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 MARMOSAIC 300 mm CCD VERTICAL FOCUSING MIRROR 2011-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-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 1.95 69.4 100 0.088 10.8 15.7 35405
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 1.95 2.02 100 0.786 15.8
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 PDB ENTRY 4ODS 1.95 69.4 35329 1767 99.7 0.199 0.197 0.2153 0.224 0.2393 RANDOM 40.78
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] 1.75 1.75 -3.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.278 r_dihedral_angle_4_deg 21.234 r_dihedral_angle_3_deg 14.677 r_dihedral_angle_1_deg 6.695 r_mcangle_it 3.389 r_mcbond_it 2.169 r_mcbond_other 2.169 r_angle_refined_deg 1.331 r_angle_other_deg 0.869 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.278 r_dihedral_angle_4_deg 21.234 r_dihedral_angle_3_deg 14.677 r_dihedral_angle_1_deg 6.695 r_mcangle_it 3.389 r_mcbond_it 2.169 r_mcbond_other 2.169 r_angle_refined_deg 1.331 r_angle_other_deg 0.869 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3375 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 63
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction