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Crystal structure of Fv fragment of anti-ciguatoxin antibody complexed with ABC-ring of ciguatoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AXS 1AXS, 1FJ1 experimental model PDB 1FJ1 1AXS, 1FJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 293 25% polyethylene glycol monomethyl ether 5000, 0.2M ammonium sulfate, 0.1M MES, 4.7% dimethylsulfoxide, 15% glycerol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.52 51.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.219 α = 90 b = 97.502 β = 90 c = 115.722 γ = 90
Symmetry Space Group I 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 ADSC QUANTUM 210 2003-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 1.7 40 98.8 0.058 6.9 29463 15.8
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 1.7 1.79 95.8 0.152 9.6 6.5 4082
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 1AXS, 1FJ1 1.7 19.72 29447 1499 98.6 0.198 0.198 0.209 0.21 0.2203 RANDOM 20.5
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] 0.12 5.6 -5.72
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.9 c_scangle_it 3.11 c_scbond_it 2.13 c_mcangle_it 1.83 c_angle_deg 1.4 c_mcbond_it 1.15 c_improper_angle_d 0.7 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.9 c_scangle_it 3.11 c_scbond_it 2.13 c_mcangle_it 1.83 c_angle_deg 1.4 c_mcbond_it 1.15 c_improper_angle_d 0.7 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1713 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 62
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction SCALA data scaling CNS phasing