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Novel binding site identified in a hybrid between cholera toxin and heat-labile enterotoxin, 1.9A crystal structure reveals the details
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EEI PDB ENTRY 1EEI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 23-24% PEG 3350, 0.25-0.3M CALCIUM CHLORIDE, 20% GLYCEROL, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 46.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.2 α = 90 b = 70.1 β = 92.9 c = 137.4 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 CCD MAR CCD 165 mm M SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.97 MAX II I711 2 ROTATING ANODE RIGAKU RU300 1.5418
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 1.94 19.44 96 0.056 19.6 5.4 77618 74812 -3.2 -3.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.94 1.99 92.94
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 1EEI 1.94 19.44 71039 71039 3773 0.18359 0.18359 0.181 0.1822 0.23179 0.234 RANDOM 23.064
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] -0.15 -2.11 -0.24 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.29 r_dihedral_angle_4_deg 22.663 r_dihedral_angle_3_deg 13.351 r_dihedral_angle_1_deg 6.735 r_scangle_it 2.772 r_scbond_it 1.811 r_angle_refined_deg 1.387 r_mcangle_it 1.244 r_mcbond_it 0.805 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.29 r_dihedral_angle_4_deg 22.663 r_dihedral_angle_3_deg 13.351 r_dihedral_angle_1_deg 6.735 r_scangle_it 2.772 r_scbond_it 1.811 r_angle_refined_deg 1.387 r_mcangle_it 1.244 r_mcbond_it 0.805 r_nbtor_refined 0.307 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7402 Nucleic Acid Atoms Solvent Atoms 888 Heterogen Atoms 570
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling