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Crystal structure of RTX domain blocks IV and V of adenylate cyclase toxin from Bordetella pertussis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M NH4NO3
20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 4.14 70.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.771 α = 90 b = 91.771 β = 90 c = 104.465 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD RAYONIX MX-225 2014-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.76 50 99.8 0.052 0.055 1 24.66 8.94 44820
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.87 99.5 0.831 0.881 0.858 2.69
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CVW 1.76 45.89 42719 2100 99.84 0.1844 0.1836 0.2008 0.203 RANDOM 35.519
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] -0.02 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.939 r_dihedral_angle_4_deg 14.261 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 6.927 r_angle_other_deg 3.978 r_mcangle_it 3.213 r_mcbond_it 2.283 r_mcbond_other 2.282 r_angle_refined_deg 1.187 r_chiral_restr 0.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.939 r_dihedral_angle_4_deg 14.261 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 6.927 r_angle_other_deg 3.978 r_mcangle_it 3.213 r_mcbond_it 2.283 r_mcbond_other 2.282 r_angle_refined_deg 1.187 r_chiral_restr 0.053 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1871 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing