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chimera of the inactive ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, with the double mutation K3528M and K3535I, fused to a proline-Rich-Domain (PRD) and profilin, bound to Latrunculin B-ADP-Mg-actin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% PEG4000 0.2M LISO4 0.1M TRIS PH8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.739 α = 90 b = 62.825 β = 91.03 c = 93.581 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 2020-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9793 SOLEIL PROXIMA 1
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 1.69 93.57 94.9 0.081 11.2 6.9 81375 30.1
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 1.69 1.85 60.1 0.91 1.7 6.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PAV 1.69 93.57 81375 4009 76.5 0.1799 0.1783 0.1818 0.2118 0.2153 RANDOM 34.97
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] -0.7148 0.5682 1.203 -0.4882
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.23 t_omega_torsion 3.3 t_angle_deg 0.92 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.23 t_omega_torsion 3.3 t_angle_deg 0.92 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6757 Nucleic Acid Atoms Solvent Atoms 958 Heterogen Atoms 122
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction autoPROC data processing Aimless data scaling STARANISO data scaling PHASER phasing XDS data reduction