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Crystal structure of Cobra 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 200mM ammonium sulfate,
100mM sodium acetate pH 4.6,
19% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.285 α = 90 b = 61.285 β = 90 c = 260.046 γ = 120
Symmetry Space Group P 32 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 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 1.8 30 98.8 0.118 0.125 0.042 4.8 8.8 53294
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 99 1.052 1.126 0.398 0.708 7.6
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 1.8 29.84 52273 973 98.88 0.16525 0.16464 0.1745 0.19811 0.2024 RANDOM 28.624
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] -0.1 -0.05 -0.1 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.907 r_dihedral_angle_3_deg 13.745 r_dihedral_angle_4_deg 13.115 r_dihedral_angle_1_deg 7.301 r_long_range_B_refined 7.08 r_long_range_B_other 6.921 r_scangle_other 5.58 r_scbond_it 3.921 r_scbond_other 3.92 r_mcangle_it 3.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.907 r_dihedral_angle_3_deg 13.745 r_dihedral_angle_4_deg 13.115 r_dihedral_angle_1_deg 7.301 r_long_range_B_refined 7.08 r_long_range_B_other 6.921 r_scangle_other 5.58 r_scbond_it 3.921 r_scbond_other 3.92 r_mcangle_it 3.383 r_mcangle_other 3.382 r_mcbond_other 2.365 r_mcbond_it 2.364 r_angle_refined_deg 1.665 r_angle_other_deg 1.435 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 3846 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction BALBES phasing