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HA1 (HA33) mutant F179I of botulinum type C progenitor toxin complexed with N-acetylgalactosamine, bound at site II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 12% ethanol, 1.7M sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.856 α = 90 b = 62.139 β = 104.47 c = 82.336 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2007-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.48 50 99.8 0.04 32.4 3.6 112188
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 1.48 1.53 98.8 0.27 4.1 2.9 11029
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 3AH2 1.48 27.48 106559 5615 99.78 0.16763 0.16632 0.1677 0.19232 0.1927 RANDOM 16.093
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.566 r_dihedral_angle_4_deg 13.098 r_dihedral_angle_3_deg 10.923 r_dihedral_angle_1_deg 7.232 r_scangle_it 2.939 r_scbond_it 1.9 r_angle_refined_deg 1.22 r_mcangle_it 1.199 r_mcbond_it 0.637 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.566 r_dihedral_angle_4_deg 13.098 r_dihedral_angle_3_deg 10.923 r_dihedral_angle_1_deg 7.232 r_scangle_it 2.939 r_scbond_it 1.9 r_angle_refined_deg 1.22 r_mcangle_it 1.199 r_mcbond_it 0.637 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4723 Nucleic Acid Atoms Solvent Atoms 922 Heterogen Atoms 15
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling