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Crystal structure of Ca2+-bound RTX domain block V of adenylate cyclase toxin from Bordetella pertussis
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 8.5 289.15 Buffer: 40 mM polyamines, 100 mM glycylglycine and 2-Amino-2-methyl-1,3-propanediol (AMPD), pH 8.5. Precipitant: 31% v/v of 10% w/v PEG 20k, 50% w/v trimethylpropane (TMP), 2% w/v NDSB-195.
Crystal Properties Matthews coefficient Solvent content 2.07 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.722 α = 90 b = 66.759 β = 93.226 c = 59.072 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2023-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 1.7 37.7 98.4 0.097 7.2 3.8 31714
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 1.7 1.73 98.2 0.991 1.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 30.664 31628 1581 98.047 0.172 0.1705 0.2082 0.1999 24.974
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] -1.744 -1.247 0.102 1.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.369 r_dihedral_angle_3_deg 14.047 r_dihedral_angle_1_deg 7.548 r_dihedral_angle_2_deg 7.263 r_lrange_it 7.122 r_scangle_it 5.69 r_scbond_it 3.687 r_mcangle_it 3.048 r_mcbond_it 2.093 r_angle_refined_deg 1.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.369 r_dihedral_angle_3_deg 14.047 r_dihedral_angle_1_deg 7.548 r_dihedral_angle_2_deg 7.263 r_lrange_it 7.122 r_scangle_it 5.69 r_scbond_it 3.687 r_mcangle_it 3.048 r_mcbond_it 2.093 r_angle_refined_deg 1.486 r_nbtor_refined 0.306 r_nbd_refined 0.223 r_symmetry_nbd_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.161 r_xyhbond_nbd_refined 0.135 r_symmetry_metal_ion_refined 0.127 r_chiral_restr 0.108 r_metal_ion_refined 0.099 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2543 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing