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Crystal Structure of the Botulinum Neurotoxin serotype G binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NP0 PDB ENTRY 2NP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 1.2 M AMSO4, 85 MM CITRATE PH 4, 8 % GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.35 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.53 α = 90 b = 93.44 β = 90 c = 131.43 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 MARRESEARCH 2008-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
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 1.9 20 98.6 0.1 11.7 4.2 40653
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 1.9 2 99.8 0.44 3.13 4.2
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 2NP0 1.9 19.83 38602 2049 98.7 0.159 0.157 0.166 0.196 0.2009 RANDOM 11.31
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 0.14 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.585 r_dihedral_angle_4_deg 14.558 r_dihedral_angle_3_deg 12.135 r_dihedral_angle_1_deg 7.051 r_scangle_it 3.073 r_scbond_it 2.148 r_angle_refined_deg 1.403 r_mcangle_it 1.229 r_mcbond_it 1.003 r_angle_other_deg 0.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.585 r_dihedral_angle_4_deg 14.558 r_dihedral_angle_3_deg 12.135 r_dihedral_angle_1_deg 7.051 r_scangle_it 3.073 r_scbond_it 2.148 r_angle_refined_deg 1.403 r_mcangle_it 1.229 r_mcbond_it 1.003 r_angle_other_deg 0.858 r_symmetry_vdw_refined 0.279 r_nbd_refined 0.2 r_nbd_other 0.193 r_nbtor_refined 0.188 r_symmetry_vdw_other 0.176 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.093 r_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3538 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing