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ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to Latrunculin-B-ATP-Mg-actin, and 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE and 2 Mg ions
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, SITTING DROP 8.5 293 26 % peg 3350, 26 % Glycerol, 30 mM LiSO4,
0.1M TrisHCl pH8.5,
3 % Dioxane,
Crystal Properties Matthews coefficient Solvent content 2.58 52.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.116 α = 90 b = 132.443 β = 110.57 c = 96.396 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 2021-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 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 2.044 47.76 84.3 0.162 14.1 32.7 86495 54.49
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 2.044 2.21 28.5 3.852
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 2.044 47.76 86494 4302 76.7 0.1916 0.19 0.188 0.2221 0.2166 RANDOM 61.71
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] 1.4461 -0.4354 -0.1995 -1.2466
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17 t_omega_torsion 3.1 t_angle_deg 0.93 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 17 t_omega_torsion 3.1 t_angle_deg 0.93 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 11956 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 200
Software Software Software Name Purpose BUSTER refinement AutoProcess data processing XDS data reduction Aimless data scaling PHASER phasing