☰ Navigation Tabs
Structure of the binding domain of BoNT/A mutant Y1117V in complex with the GD1a ganglioside receptor
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 293 100mM Phosphate/Citrate pH 4.2
36% PEG300
Crystal Properties Matthews coefficient Solvent content 2.23 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.531 α = 90 b = 104.421 β = 90 c = 112.889 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 PIXEL DECTRIS PILATUS 6M-F 2015-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.9 55.01 99.8 0.097 0.064 0.977 9.4 6 69000
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 99.9 0.618 0.743 0.407 0.723 2.7 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 55.01 65552 3374 99.7 0.21956 0.21751 0.2219 0.25971 0.262 RANDOM 27.229
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] 1.17 -0.24 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.658 r_dihedral_angle_4_deg 17.157 r_dihedral_angle_3_deg 13.488 r_dihedral_angle_1_deg 7.407 r_long_range_B_refined 3.587 r_long_range_B_other 3.534 r_mcangle_it 1.713 r_mcangle_other 1.713 r_scangle_other 1.703 r_angle_refined_deg 1.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.658 r_dihedral_angle_4_deg 17.157 r_dihedral_angle_3_deg 13.488 r_dihedral_angle_1_deg 7.407 r_long_range_B_refined 3.587 r_long_range_B_other 3.534 r_mcangle_it 1.713 r_mcangle_other 1.713 r_scangle_other 1.703 r_angle_refined_deg 1.462 r_scbond_it 0.998 r_scbond_other 0.997 r_mcbond_it 0.986 r_mcbond_other 0.985 r_angle_other_deg 0.91 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6810 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing