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HA3 subcomponent of Clostridium botulinum type C progenitor toxin, complex with N-acetylneuramic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 293 1.2M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 5.331016 76.927475
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.076 α = 90 b = 177.076 β = 90 c = 81.042 γ = 120
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 210 2007-06-12 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 2.6 50 99.9 0.066 41.9 50275 44733 48.4
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) 2.6 2.69 100 0.416 5
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 2Z5A 2.6 33.21 50254 44713 4507 99.9 0.234 0.234 0.2343 0.253 0.2532 RANDOM 56.7
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] 6.88 6.88 -13.77
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.7 c_scangle_it 2.68 c_mcangle_it 2.37 c_improper_angle_d 1.94 c_scbond_it 1.73 c_mcbond_it 1.35 c_angle_deg 1.1 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.7 c_scangle_it 2.68 c_mcangle_it 2.37 c_improper_angle_d 1.94 c_scbond_it 1.73 c_mcbond_it 1.35 c_angle_deg 1.1 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4706 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 21
Software Software Software Name Purpose CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing