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RTX domain block V of adenylate cyclase toxin with mutations D1533N, A1542N, D1560N, S1569N, D1587N, H1598N, H1608N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 Buffer: 0.1 M MES, 0.1 M imidazole, pH 6.5
Precipitant: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 0.02 M of each amino acid (L-glutamate, DL-alanine, glycine, DL-lysine, and DL-serine)
Protein solution: 50 mM Tris, 150 mM NaCl, 10 mM CaCl2, pH 8
Crystal Properties Matthews coefficient Solvent content 2.05 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.305 α = 84.13 b = 38.003 β = 81.47 c = 57.016 γ = 67.61
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 XE 16M 2024-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 1.99 30.58 85.4 0.103 6.6 3.8 14967 18.2
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 1.99 2.04 85.3 0.292
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 (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 FREE R-VALUE 1.99 30.58 14115 766 85.45 0.23164 0.22847 0.2285 0.29235 0.2928 RANDOM 38.338
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] -1.82 1.07 -1.03 -0.42 1.34 2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.155 r_dihedral_angle_1_deg 8.578 r_long_range_B_refined 7.52 r_dihedral_angle_2_deg 4.605 r_mcangle_it 4.026 r_scbond_it 3.427 r_mcbond_it 2.633 r_angle_refined_deg 1.317 r_chiral_restr 0.111 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.155 r_dihedral_angle_1_deg 8.578 r_long_range_B_refined 7.52 r_dihedral_angle_2_deg 4.605 r_mcangle_it 4.026 r_scbond_it 3.427 r_mcbond_it 2.633 r_angle_refined_deg 1.317 r_chiral_restr 0.111 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2276 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing