☰ Navigation Tabs
Crystal Structure of the Botulinum Neurotoxin Serotype A binding domain
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 5.2 18% PEG3350, 0.2 M MGCL2, 0.1 M BISTRIS PH 5.2
Crystal Properties Matthews coefficient Solvent content 2.21 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73 α = 90 b = 114.5 β = 90 c = 105.8 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 2007-11-18 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 1.7 20 99 0.04 27 7.8 48513
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 1.7 1.8 98.4 0.53 4.2 7.5
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 1.7 19.73 46044 2469 99 0.17 0.168 0.1787 0.205 0.2114 RANDOM 19.73
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] 0.95 0.13 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.931 r_dihedral_angle_4_deg 16.08 r_dihedral_angle_3_deg 13.638 r_dihedral_angle_1_deg 7.281 r_scangle_it 3.185 r_scbond_it 2.283 r_angle_refined_deg 1.478 r_mcangle_it 1.374 r_mcbond_it 1.11 r_angle_other_deg 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.931 r_dihedral_angle_4_deg 16.08 r_dihedral_angle_3_deg 13.638 r_dihedral_angle_1_deg 7.281 r_scangle_it 3.185 r_scbond_it 2.283 r_angle_refined_deg 1.478 r_mcangle_it 1.374 r_mcbond_it 1.11 r_angle_other_deg 0.88 r_symmetry_vdw_other 0.283 r_symmetry_hbond_refined 0.234 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.201 r_nbd_other 0.198 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.092 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 3487 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing