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Cholera toxin A1 subunit bound to its substrate, NAD+, and its human protein activator, ARF6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A5D CTA1:ARF6-GTP
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 2.38 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.905 α = 90 b = 90.925 β = 90 c = 98.001 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 CUSTOM-MADE 2004-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 0.97943 APS 32-ID
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 2.02 50 97.5 25861 25861 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 2.02 2.09 81.7
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 (All) 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 Isomorphous replacement THROUGHOUT CTA1:ARF6-GTP 2.02 43.15 24930 24930 1329 96.79 0.233 0.18369 0.18114 0.1896 0.23075 0.2343 RANDOM 36.241
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] 0.01 -0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.041 r_dihedral_angle_4_deg 18.162 r_dihedral_angle_3_deg 14.168 r_dihedral_angle_1_deg 6.546 r_mcangle_it 2.421 r_scangle_it 2.169 r_angle_refined_deg 1.561 r_mcbond_it 1.438 r_scbond_it 1.399 r_angle_other_deg 0.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.041 r_dihedral_angle_4_deg 18.162 r_dihedral_angle_3_deg 14.168 r_dihedral_angle_1_deg 6.546 r_mcangle_it 2.421 r_scangle_it 2.169 r_angle_refined_deg 1.561 r_mcbond_it 1.438 r_scbond_it 1.399 r_angle_other_deg 0.773 r_symmetry_vdw_other 0.297 r_mcbond_other 0.285 r_symmetry_hbond_refined 0.241 r_xyhbond_nbd_refined 0.217 r_nbd_refined 0.214 r_nbd_other 0.206 r_nbtor_refined 0.189 r_symmetry_vdw_refined 0.122 r_chiral_restr 0.09 r_nbtor_other 0.09 r_metal_ion_refined 0.082 r_xyhbond_nbd_other 0.075 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2740 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction CCP4 data scaling