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Crystal structure of HA3 from Clostridium botulinum type B with alpha2,3-sialyllactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 295 14% PEG 3350 and 0.1 M BisTris HCl pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.974 α = 90 b = 144.091 β = 90 c = 158.032 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX225HE 2012-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.8 SPring-8 BL44XU
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 3 50 90.4 0.105 7.1 3.6 34819
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 3 3.11 88.2 0.501 3.1 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3 44.32 32677 1749 90.01 0.2277 0.22379 0.2289 0.30258 0.2952 RANDOM 62.961
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] 0.12 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.679 r_long_range_B_refined 10.84 r_long_range_B_other 10.84 r_dihedral_angle_2_deg 8.373 r_dihedral_angle_1_deg 7.974 r_mcangle_it 7.6 r_mcangle_other 7.599 r_scangle_other 7.376 r_mcbond_it 4.753 r_mcbond_other 4.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.679 r_long_range_B_refined 10.84 r_long_range_B_other 10.84 r_dihedral_angle_2_deg 8.373 r_dihedral_angle_1_deg 7.974 r_mcangle_it 7.6 r_mcangle_other 7.599 r_scangle_other 7.376 r_mcbond_it 4.753 r_mcbond_other 4.753 r_scbond_it 4.541 r_scbond_other 4.541 r_angle_refined_deg 1.362 r_angle_other_deg 0.479 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13576 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling DENZO data reduction MOLREP phasing PDB_EXTRACT data extraction