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Structural Basis for Ligand Recognition and Discrimination of a Quorum Quenching Antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 15C8 PDB ENTRY 15C8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 20 % PEG 4000, 0.2 M di-ammonium hydrogen phosphate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.93 58.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.182 α = 90 b = 183.182 β = 90 c = 42.594 γ = 120
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 MAR 300 CCD 2007-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
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 2.78 91.67 97.9 0.108 7.7 2.3 13033 13033 -3 41.2
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 2.78 2.854 94 0.408 1.9 2.1 840
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 (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 15C8 2.78 91.67 13033 13033 644 97.21 0.19685 0.19464 0.1989 0.24028 0.2449 RANDOM 53.305
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] 0.41 0.21 0.41 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.858 r_dihedral_angle_3_deg 14.284 r_dihedral_angle_4_deg 14.022 r_dihedral_angle_1_deg 6.508 r_angle_other_deg 1.408 r_angle_refined_deg 1.207 r_scangle_it 1.186 r_scbond_it 0.663 r_mcangle_it 0.634 r_mcbond_it 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.858 r_dihedral_angle_3_deg 14.284 r_dihedral_angle_4_deg 14.022 r_dihedral_angle_1_deg 6.508 r_angle_other_deg 1.408 r_angle_refined_deg 1.207 r_scangle_it 1.186 r_scbond_it 0.663 r_mcangle_it 0.634 r_mcbond_it 0.338 r_chiral_restr 0.054 r_mcbond_other 0.033 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3272 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 28
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling