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Crystal structure of Black mamba toxin in complex with Centi-SNX-B03 antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Tris pH 8.5, 20% PEG4000, 0.2M Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 3.11 60.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.539 α = 90 b = 72.252 β = 91.99 c = 179.656 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2023-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.979497 APS 22-ID
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 1.8 30.01 98.8 0.047 0.056 0.029 0.998 11.1 3.7 121160
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 1.8 1.86 98 0.809 0.941 0.475 0.711 3.8
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 1.8 30.01 119970 1158 98.62 0.18163 0.18119 0.1901 0.22943 0.234 RANDOM 36.144
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] 1.85 -0.33 -0.46 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.71 r_dihedral_angle_4_deg 17.84 r_dihedral_angle_3_deg 15.106 r_long_range_B_refined 9.096 r_long_range_B_other 9.039 r_dihedral_angle_1_deg 7.819 r_scangle_other 6.52 r_mcangle_other 5.134 r_mcangle_it 5.133 r_scbond_it 4.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.71 r_dihedral_angle_4_deg 17.84 r_dihedral_angle_3_deg 15.106 r_long_range_B_refined 9.096 r_long_range_B_other 9.039 r_dihedral_angle_1_deg 7.819 r_scangle_other 6.52 r_mcangle_other 5.134 r_mcangle_it 5.133 r_scbond_it 4.34 r_scbond_other 4.339 r_mcbond_it 3.526 r_mcbond_other 3.523 r_angle_refined_deg 1.704 r_angle_other_deg 1.398 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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 7409 Nucleic Acid Atoms Solvent Atoms 860 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction BALBES phasing