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Structure of S55-3 Fab in complex with Lipid A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ODS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 289 1M LiCl, 0.1M citric acid, and 20% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.32 47.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 338.121 α = 90 b = 52.865 β = 100.95 c = 75.391 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate OSMIC BLUE MIRRORS 2013-04-30 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 1.95 25 98.7 0.092 9 4.1 94048
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 98.7 0.577 4.2 9294
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ODS 1.95 25 89318 4730 98.27 0.2139 0.2122 0.2453 0.2628 RANDOM 38.843
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] 0.02 0.75 -0.71 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.599 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 16.794 r_dihedral_angle_1_deg 6.555 r_mcangle_it 3.441 r_mcbond_it 2.293 r_mcbond_other 2.293 r_angle_refined_deg 1.472 r_angle_other_deg 1.109 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.599 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 16.794 r_dihedral_angle_1_deg 6.555 r_mcangle_it 3.441 r_mcbond_it 2.293 r_mcbond_other 2.293 r_angle_refined_deg 1.472 r_angle_other_deg 1.109 r_chiral_restr 0.109 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9801 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 113
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction