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HA1 subcomponent of botulinum type C progenitor toxin complexed with N-acetylgalactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QXM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 12% ethanol, 1.7M sodium chloride, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.937 α = 90 b = 62.061 β = 104.22 c = 82.426 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 4 2006-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0 Photon Factory BL-6A
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 1.7 50 99.9 0.056 21.8 3.6 74218 74218 15.7
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) 1.7 1.76 99.6 0.312 4.1 3.6 7373
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 1QXM 1.7 43.93 66722 7496 99.64 0.17673 0.17375 0.174 0.20325 0.2033 RANDOM 21.552
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.843 r_dihedral_angle_4_deg 16.28 r_dihedral_angle_3_deg 11.836 r_dihedral_angle_1_deg 7.201 r_scangle_it 2.903 r_scbond_it 1.802 r_mcangle_it 1.219 r_angle_refined_deg 1.191 r_mcbond_it 0.641 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.843 r_dihedral_angle_4_deg 16.28 r_dihedral_angle_3_deg 11.836 r_dihedral_angle_1_deg 7.201 r_scangle_it 2.903 r_scbond_it 1.802 r_mcangle_it 1.219 r_angle_refined_deg 1.191 r_mcbond_it 0.641 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 4720 Nucleic Acid Atoms Solvent Atoms 788 Heterogen Atoms 15
Software Software Software Name Purpose ADSC data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing