☰ Navigation Tabs
Crystal Structure of botulinum neurotoxin A2 cell binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 289.15 0.1m Sodium acetate, 4.55% PEG 400, 4.55% PEG 500 MME, 4.55% PEG 600, 4.55% PEG 1000, 4.55% PEG 2000, 4.55% PEG 3350, 4.55% PEG 4000, 4.55% PEG 5000, 4.55% PEG 6000, 4.55% PEG 8000, 4.55% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.918 α = 90 b = 100.786 β = 90 c = 116.151 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 EIGER2 XE 16M 2021-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.63 116.15 100 0.159 0.031 0.999 11.6 26.3 59567
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.66 99.9 5.53 1.087 0.299 26.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5MOY 1.63 76.123 59446 2962 99.928 0.205 0.203 0.209 0.2367 0.2392 30.782
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] 1.613 -0.806 -0.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.34 r_dihedral_angle_3_deg 13.407 r_dihedral_angle_4_deg 12.029 r_dihedral_angle_other_3_deg 10.101 r_dihedral_angle_1_deg 7.81 r_lrange_it 6.847 r_lrange_other 6.833 r_scangle_it 5.465 r_scangle_other 5.464 r_scbond_it 3.699
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.34 r_dihedral_angle_3_deg 13.407 r_dihedral_angle_4_deg 12.029 r_dihedral_angle_other_3_deg 10.101 r_dihedral_angle_1_deg 7.81 r_lrange_it 6.847 r_lrange_other 6.833 r_scangle_it 5.465 r_scangle_other 5.464 r_scbond_it 3.699 r_scbond_other 3.698 r_mcangle_it 3.624 r_mcangle_other 3.624 r_mcbond_it 2.61 r_mcbond_other 2.606 r_angle_refined_deg 1.602 r_angle_other_deg 1.371 r_symmetry_nbd_refined 0.297 r_nbd_refined 0.192 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.172 r_nbd_other 0.149 r_xyhbond_nbd_refined 0.134 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3339 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing