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Crystal Structure of Quorum-Quenching Antibody 1G9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NTF PDB entry 2NTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 10% (w/v) PEG 8000, 0.1M Imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.53 51.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.925 α = 90 b = 72.041 β = 90 c = 116.143 γ = 90
Symmetry Space Group P 21 21 21
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 325 mm CCD Flat mirror (vertical focusing) 2007-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.03317 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.85 50 99.6 0.062 26.1 3.6 11938 11938 83.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.924 99.9 0.534 2.7 3.6 782
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 (All) 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 2NTF 2.85 35.4 11064 11064 556 99.65 0.20255 0.20255 0.19959 0.1985 0.26329 0.2712 RANDOM 50.953
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] -0.47 0.71 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.126 r_dihedral_angle_3_deg 18.421 r_dihedral_angle_4_deg 12.196 r_dihedral_angle_1_deg 7.462 r_scangle_it 1.599 r_angle_refined_deg 1.488 r_scbond_it 1.06 r_angle_other_deg 0.837 r_mcangle_it 0.721 r_mcbond_it 0.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.126 r_dihedral_angle_3_deg 18.421 r_dihedral_angle_4_deg 12.196 r_dihedral_angle_1_deg 7.462 r_scangle_it 1.599 r_angle_refined_deg 1.488 r_scbond_it 1.06 r_angle_other_deg 0.837 r_mcangle_it 0.721 r_mcbond_it 0.527 r_symmetry_vdw_other 0.302 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.227 r_nbd_other 0.215 r_nbtor_refined 0.2 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.128 r_nbtor_other 0.096 r_chiral_restr 0.079 r_mcbond_other 0.079 r_xyhbond_nbd_other 0.041 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3277 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing