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The allosteric binding mode of alphaD-conotoxin VxXXB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296.15 0.91 M lithium chloride, 16% PEG6000 and 0.1 M MES monohydrate pH 6.4
Crystal Properties Matthews coefficient Solvent content 2.48 50.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.909 α = 90 b = 119.573 β = 90 c = 150.733 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 EIGER X 16M 2020-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95365 Australian Synchrotron MX2
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 2.47 46.36 99.4 0.066 11.5 6.7 45467
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 2.47 2.55 1.178
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5T90 2.47 46.36 41036 1876 94.04 0.20033 0.19826 0.24635 0.2426 RANDOM 81.488
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] 0.52 -0.62 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.481 r_dihedral_angle_4_deg 20.897 r_dihedral_angle_3_deg 18.001 r_dihedral_angle_1_deg 8.152 r_long_range_B_other 7.908 r_long_range_B_refined 7.907 r_scangle_other 5.09 r_mcangle_it 4.428 r_mcangle_other 4.428 r_scbond_it 3.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.481 r_dihedral_angle_4_deg 20.897 r_dihedral_angle_3_deg 18.001 r_dihedral_angle_1_deg 8.152 r_long_range_B_other 7.908 r_long_range_B_refined 7.907 r_scangle_other 5.09 r_mcangle_it 4.428 r_mcangle_other 4.428 r_scbond_it 3.248 r_scbond_other 3.248 r_mcbond_it 2.76 r_mcbond_other 2.76 r_angle_refined_deg 1.813 r_angle_other_deg 1.129 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8772 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHENIX phasing