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Crystal structure of Mamba alpha-neurotoxin in complex with Centi-LNX-D09 antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Model found by BALBES software using input sequence
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1M Tris pH 8.5,
10% PEG4000,
50mM Proline
Crystal Properties Matthews coefficient Solvent content 2.39 48.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.703 α = 90 b = 145.537 β = 104.9 c = 64.207 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 EIGER X 16M 2021-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 30 94.7 0.241 0.296 0.168 5.6 2.8 50268
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 2.28 80.8 0.63 0.841 0.552 0.543 1.7
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 Model found by BALBES software using input sequence 2.2 29.78 49249 989 94.24 0.19746 0.19641 0.2033 0.24848 0.2497 RANDOM 23.638
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] 2.51 -0.16 -1.59 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.76 r_dihedral_angle_4_deg 18.9 r_dihedral_angle_3_deg 16.168 r_dihedral_angle_1_deg 8.129 r_long_range_B_refined 5.668 r_long_range_B_other 5.55 r_scangle_other 3.462 r_mcangle_it 2.877 r_mcangle_other 2.876 r_scbond_it 2.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.76 r_dihedral_angle_4_deg 18.9 r_dihedral_angle_3_deg 16.168 r_dihedral_angle_1_deg 8.129 r_long_range_B_refined 5.668 r_long_range_B_other 5.55 r_scangle_other 3.462 r_mcangle_it 2.877 r_mcangle_other 2.876 r_scbond_it 2.132 r_scbond_other 2.132 r_mcbond_it 1.764 r_mcbond_other 1.756 r_angle_refined_deg 1.529 r_angle_other_deg 1.251 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 7397 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction BALBES phasing