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Binding domain of BoNT/A complexed with ganglioside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VU9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 20% PEG6000, 0.2 M MgCl2, 0.1 M Hepes pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.26 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.972 α = 90 b = 114.302 β = 90 c = 106.495 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 225 mm CCD 2011-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.92526 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 63 98.3 0.121 0.078 0.986 10 3.5 30186
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99 0.565 0.356 0.742 2.6 3.5 2228
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2VU9 2 62.1 28636 1532 97.74 0.2045 0.2027 0.238 0.2121 RANDOM 27.222
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] 0.13 0.06 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.192 r_dihedral_angle_4_deg 20.954 r_dihedral_angle_3_deg 15.001 r_dihedral_angle_1_deg 6.623 r_mcangle_it 1.742 r_angle_refined_deg 1.356 r_scbond_it 1.231 r_mcbond_it 0.97 r_chiral_restr 0.086 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.192 r_dihedral_angle_4_deg 20.954 r_dihedral_angle_3_deg 15.001 r_dihedral_angle_1_deg 6.623 r_mcangle_it 1.742 r_angle_refined_deg 1.356 r_scbond_it 1.231 r_mcbond_it 0.97 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3501 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction