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HA1 subcomponent of botulinum type C progenitor toxin complexed with galactose
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 2.5 50.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.921 α = 90 b = 62.176 β = 104.75 c = 82.27 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 2006-05-11 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 1.78 50 97.5 0.043 31.3 3.8 63127 63127 13.9
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) 1.78 1.84 91.2 0.211 6.8 3.7 5877
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 1.78 39.78 56829 6387 97.49 0.16783 0.16412 0.1643 0.20089 0.1995 RANDOM 21.485
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 39.707 r_dihedral_angle_4_deg 13.373 r_dihedral_angle_3_deg 12.266 r_dihedral_angle_1_deg 7.224 r_scangle_it 2.915 r_scbond_it 1.801 r_mcangle_it 1.175 r_angle_refined_deg 1.171 r_mcbond_it 0.615 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.707 r_dihedral_angle_4_deg 13.373 r_dihedral_angle_3_deg 12.266 r_dihedral_angle_1_deg 7.224 r_scangle_it 2.915 r_scbond_it 1.801 r_mcangle_it 1.175 r_angle_refined_deg 1.171 r_mcbond_it 0.615 r_chiral_restr 0.081 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 4735 Nucleic Acid Atoms Solvent Atoms 760 Heterogen Atoms 24
Software Software Software Name Purpose ADSC data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing