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Crystal structure of Sr2+-bound RTX domain block V of adenylate cyclase toxin from Bordetella pertussis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 Buffer: 100 mM amino acids, 100 mM imidazole, 100 mM 2-(N-morpholino)ethanesulfonic
acid (MES), pH 6.5.
Precipitant: 37.5% v/v of 25% v/v 2-Methyl-2,4-pentanediol (MPD), 25% w/v PEG 1000, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.54 α = 90 b = 73.095 β = 90 c = 73.839 γ = 90
Symmetry Space Group I 2 2 2
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 2024-05-16 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.76910 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 1.5 30.95 98.6 0.303 5 13.2 26872 15.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 94.2 1.86 2.03 1.2
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 MAD FREE R-VALUE 1.502 30.949 26846 1314 98.089 0.176 0.1745 0.1877 0.2014 0.2115 21.48
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] -1.424 -0.758 2.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.595 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_2_deg 8.612 r_lrange_it 7.728 r_dihedral_angle_1_deg 6.86 r_scangle_it 5.852 r_scbond_it 4.038 r_mcangle_it 3.053 r_mcbond_it 2.048 r_angle_refined_deg 1.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.595 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_2_deg 8.612 r_lrange_it 7.728 r_dihedral_angle_1_deg 6.86 r_scangle_it 5.852 r_scbond_it 4.038 r_mcangle_it 3.053 r_mcbond_it 2.048 r_angle_refined_deg 1.768 r_symmetry_nbd_refined 0.357 r_nbtor_refined 0.315 r_nbd_refined 0.265 r_metal_ion_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.201 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.128 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1145 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement DIALS data reduction SCALA data scaling CRANK2 phasing