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Binding domain of botulinum neurotoxin E in complex with GD1a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 294 0.2 M sodium chloride 0.1 M phosphate/citrate pH 4.2, 20 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.2 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.372 α = 90 b = 84.92 β = 91.565 c = 79.903 γ = 90
Symmetry Space Group P 1 21 1
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 2015-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.2 53.77 95.4 0.066 0.094 0.066 0.987 7.5 3 44975 34.8
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 2.2 2.27 92.5 0.529 0.748 0.529 0.807 1.7 2.8
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3FFZ 2.2 53.77 44952 2082 95.245 0.219 0.2165 0.2709 0.2704 40.213
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] -2.981 1.159 3.566 -0.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.605 r_dihedral_angle_4_deg 15.544 r_dihedral_angle_3_deg 12.449 r_dihedral_angle_1_deg 7.28 r_lrange_it 4.37 r_lrange_other 4.352 r_mcangle_it 2.728 r_mcangle_other 2.728 r_scangle_it 2.466 r_scangle_other 2.466
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.605 r_dihedral_angle_4_deg 15.544 r_dihedral_angle_3_deg 12.449 r_dihedral_angle_1_deg 7.28 r_lrange_it 4.37 r_lrange_other 4.352 r_mcangle_it 2.728 r_mcangle_other 2.728 r_scangle_it 2.466 r_scangle_other 2.466 r_mcbond_it 1.569 r_mcbond_other 1.569 r_scbond_it 1.409 r_scbond_other 1.409 r_angle_refined_deg 1.212 r_angle_other_deg 1.077 r_nbd_refined 0.162 r_symmetry_nbd_other 0.162 r_nbtor_refined 0.158 r_nbd_other 0.154 r_symmetry_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.138 r_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.064 r_chiral_restr 0.039 r_gen_planes_refined 0.003 r_symmetry_xyhbond_nbd_other 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6634 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing