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Structure of the cytoplasmic domain of csx23 from Vibrio cholera in complex with cyclic tetra-adenylate (cA4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.2MLiS04, 0.1M NaAcetate, 42.5% peg400
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.425 α = 90 b = 66.425 β = 90 c = 42.479 γ = 90
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 EIGER2 X 16M 2022-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.76 46.97 89.1 1 14.3 13.3 5251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.91 0.721
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.761 46.97 5251 218 56.615 0.245 0.2433 0.2481 0.2724 0.2699 41.01
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] 0.049 0.049 -0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.408 r_dihedral_angle_3_deg 13.582 r_dihedral_angle_6_deg 13.063 r_dihedral_angle_1_deg 6.951 r_lrange_it 6.512 r_lrange_other 6.494 r_mcangle_it 4.312 r_mcangle_other 4.307 r_scangle_it 3.29 r_scangle_other 3.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.408 r_dihedral_angle_3_deg 13.582 r_dihedral_angle_6_deg 13.063 r_dihedral_angle_1_deg 6.951 r_lrange_it 6.512 r_lrange_other 6.494 r_mcangle_it 4.312 r_mcangle_other 4.307 r_scangle_it 3.29 r_scangle_other 3.287 r_mcbond_it 2.55 r_mcbond_other 2.546 r_scbond_it 1.934 r_scbond_other 1.932 r_angle_refined_deg 1.112 r_angle_other_deg 0.947 r_symmetry_nbd_other 0.197 r_nbd_refined 0.194 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.146 r_nbd_other 0.139 r_symmetry_nbd_refined 0.111 r_symmetry_xyhbond_nbd_refined 0.103 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.049 r_bond_other_d 0.042 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 619 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing