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Structural basis for the activation of cholera toxin by human ARF6-GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O3Y 1. mouse ARF1 (1O3Y) 2. CTA1 (1S5E) experimental model PDB 1S5E 1. mouse ARF1 (1O3Y) 2. CTA1 (1S5E)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 PEG2000mme, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.915 α = 90 b = 91.446 β = 90 c = 98.547 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2004-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0781 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 93.3 36064 36064 1.5 1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 56.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1. mouse ARF1 (1O3Y)
2. CTA1 (1S5E) 1.8 45.74 34206 34206 1798 93.34 0.16855 0.16686 0.1781 0.19939 0.2048 RANDOM 21.063
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] 0.3 -0.05 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.837 r_dihedral_angle_4_deg 18.044 r_dihedral_angle_3_deg 13.128 r_dihedral_angle_1_deg 6.128 r_scangle_it 2.708 r_mcangle_it 2.495 r_angle_refined_deg 2.025 r_scbond_it 1.87 r_mcbond_it 1.578 r_angle_other_deg 0.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.837 r_dihedral_angle_4_deg 18.044 r_dihedral_angle_3_deg 13.128 r_dihedral_angle_1_deg 6.128 r_scangle_it 2.708 r_mcangle_it 2.495 r_angle_refined_deg 2.025 r_scbond_it 1.87 r_mcbond_it 1.578 r_angle_other_deg 0.869 r_mcbond_other 0.449 r_symmetry_vdw_other 0.357 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.231 r_nbd_other 0.219 r_nbtor_refined 0.19 r_xyhbond_nbd_other 0.165 r_symmetry_vdw_refined 0.161 r_chiral_restr 0.115 r_nbtor_other 0.101 r_metal_ion_refined 0.09 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2762 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing