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Binding domain of Botulinum Neurotoxin DC in complex with SialylT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ISQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M Ammonium Nitrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.16 61.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.699 α = 90 b = 109.699 β = 90 c = 210.461 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.98405 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.59 48.64 99.2 0.239 0.996 13.2 14.5 40710
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.69 92.6 1.437 0.789 13.1
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 4ISQ 2.59 48.64 38598 2032 99.18 0.2086 0.2074 0.211 0.2309 0.2329 RANDOM 40.977
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] -2.03 -2.03 4.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.694 r_dihedral_angle_4_deg 17.922 r_dihedral_angle_3_deg 13.811 r_dihedral_angle_1_deg 6.313 r_mcangle_it 2.867 r_mcbond_it 1.622 r_mcbond_other 1.622 r_angle_refined_deg 1.175 r_angle_other_deg 0.921 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.694 r_dihedral_angle_4_deg 17.922 r_dihedral_angle_3_deg 13.811 r_dihedral_angle_1_deg 6.313 r_mcangle_it 2.867 r_mcbond_it 1.622 r_mcbond_other 1.622 r_angle_refined_deg 1.175 r_angle_other_deg 0.921 r_chiral_restr 0.101 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6709 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 92
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction