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Heterodimer formation of sensory domains of Vibrio cholerae regulators ToxR and ToxS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold Model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 30mg/ml of ToxRSp in Tris buffer (20mM Tris, 150mM NaCl, pH7), 0.5 microliters of protein was mixed with 0.5 microliters of crystal condition (0.2 M Magnesium chloride hexahydrate. 0.1 M BIS-Tris. 5.5. 25 % w/v PEG 3350)
Crystal Properties Matthews coefficient Solvent content 1.99 38.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.507 α = 90 b = 72.507 β = 90 c = 79.463 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 PIXEL DECTRIS EIGER X 4M 2016-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.967700 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3 62.793 100 0.108 0.123 0.059 0.999 12.8 8.1 4790
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.18 0.842 0.966 0.466 0.688 7.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Alphafold Model 3.002 62.793 4787 260 99.896 0.215 0.2129 0.2129 0.2529 0.2529 87.359
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] -0.922 -0.461 -0.922 2.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 22.217 r_dihedral_angle_3_deg 15.155 r_lrange_it 14.783 r_scangle_it 10.551 r_mcangle_it 8.9 r_dihedral_angle_1_deg 7.941 r_scbond_it 6.724 r_mcbond_it 5.626 r_angle_refined_deg 1.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 22.217 r_dihedral_angle_3_deg 15.155 r_lrange_it 14.783 r_scangle_it 10.551 r_mcangle_it 8.9 r_dihedral_angle_1_deg 7.941 r_scbond_it 6.724 r_mcbond_it 5.626 r_angle_refined_deg 1.749 r_symmetry_xyhbond_nbd_refined 0.428 r_symmetry_nbd_refined 0.342 r_nbtor_refined 0.293 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.071 r_bond_refined_d 0.013 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1854 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing