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Crystal structure of hemagglutinin subcomponent complex (HA-33/HA-17) from Clostridium botulinum serotype D strain 4947
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QXM PDB ENTRY 1QXM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 7% PEG 8000, 0.1M MES, 0.1M Magnesium Chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.27 62.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 239.132 α = 90 b = 239.132 β = 90 c = 100.024 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 IMAGE PLATE RIGAKU RAXIS VII RIGAKU MaxScreen 2006-04-21 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD RIGAKU JUPITER 210 2006-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418 2 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
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 1.85 119.52 99.8 92648 25.8
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 PDB ENTRY 1QXM 1.85 49.81 87820 4626 99.78 0.19553 0.19372 0.1921 0.22879 0.2268 RANDOM 26.865
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] 0.21 0.1 0.21 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.363 r_dihedral_angle_4_deg 17.461 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_1_deg 8.069 r_scangle_it 3.353 r_scbond_it 2.285 r_mcangle_it 1.578 r_angle_refined_deg 1.48 r_mcbond_it 0.962 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.363 r_dihedral_angle_4_deg 17.461 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_1_deg 8.069 r_scangle_it 3.353 r_scbond_it 2.285 r_mcangle_it 1.578 r_angle_refined_deg 1.48 r_mcbond_it 0.962 r_nbtor_refined 0.302 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.12 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 5913 Nucleic Acid Atoms Solvent Atoms 718 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection XTALVIEW refinement