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Unliganded Fab structure of lipid A-specific antibody A6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ODV PDB ENTRY 4ODV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 0.1M Tris-HCl, 35% (w/v) PEG 1000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.9 35.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.129 α = 70.99 b = 69.235 β = 72.39 c = 69.066 γ = 88.29
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 0.9794 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 2.7 65.27 98.1 0.04 15.4 2 36601 18489
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 2.7 2.8 98.3 0.472 2 1892
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 4ODV 2.72 65.27 16440 833 86.61 0.2325 0.2313 0.2331 0.2566 0.2573 RANDOM 53.3046
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] -0.22 1.13 0.96 4.59 0.69 -2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.094 r_dihedral_angle_3_deg 19.648 r_dihedral_angle_4_deg 18.083 r_dihedral_angle_1_deg 7.863 r_angle_other_deg 2.149 r_angle_refined_deg 1.613 r_mcangle_it 0.584 r_mcbond_it 0.364 r_mcbond_other 0.364 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.094 r_dihedral_angle_3_deg 19.648 r_dihedral_angle_4_deg 18.083 r_dihedral_angle_1_deg 7.863 r_angle_other_deg 2.149 r_angle_refined_deg 1.613 r_mcangle_it 0.584 r_mcbond_it 0.364 r_mcbond_other 0.364 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6534 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Macromolecular data collection HKL-2000 data reduction