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CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE A BINDING DOMAIN IN COMPLEX WITH GT1B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NYY PDB ENTRY 2NYY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 21% PEG3350, 0.2 M MGCL2, 0.1 M BISTRIS PH5.5
Crystal Properties Matthews coefficient Solvent content 2.23 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.7 α = 90 b = 116.11 β = 90 c = 105.52 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 MARRESEARCH 2007-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 1.6 20 99.6 0.04 27 7.4 58845
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 1.6 1.7 99.2 0.4 5.3 7.3
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 2NYY 1.6 19.67 55875 2968 99.6 0.162 0.161 0.171 0.186 0.1964 RANDOM 13.7
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] 0.02 0.39 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.519 r_dihedral_angle_4_deg 16.003 r_dihedral_angle_3_deg 12.869 r_dihedral_angle_1_deg 7.301 r_scangle_it 3.21 r_scbond_it 2.303 r_angle_refined_deg 1.455 r_mcangle_it 1.298 r_mcbond_it 1.08 r_angle_other_deg 0.852
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.519 r_dihedral_angle_4_deg 16.003 r_dihedral_angle_3_deg 12.869 r_dihedral_angle_1_deg 7.301 r_scangle_it 3.21 r_scbond_it 2.303 r_angle_refined_deg 1.455 r_mcangle_it 1.298 r_mcbond_it 1.08 r_angle_other_deg 0.852 r_symmetry_vdw_other 0.205 r_nbd_refined 0.199 r_nbd_other 0.198 r_symmetry_vdw_refined 0.196 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.129 r_nbtor_other 0.097 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 3501 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing