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Crystal structure of the catalytic domain of botulinum neurotoxin X
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EPW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 PEG1500, MMT
Crystal Properties Matthews coefficient Solvent content 2 37.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.34 α = 90 b = 86.732 β = 90 c = 93.079 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 PILATUS 6M-F 2016-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 1.35 63.45 99.8 0.083 0.098 0.053 0.997 9.2 6.3 98954
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 1.35 1.37 64.8 0.981 1.23 0.738 0.417 1 3.9
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 1epw 1.35 63.45 93863 4986 94.87 0.14458 0.14291 0.1428 0.17617 0.176 RANDOM 20.599
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] 1.64 -1.01 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.895 r_sphericity_free 29.397 r_dihedral_angle_4_deg 14.566 r_dihedral_angle_3_deg 10.956 r_sphericity_bonded 9.939 r_dihedral_angle_1_deg 8.697 r_long_range_B_refined 4.025 r_long_range_B_other 3.237 r_scangle_other 2.222 r_mcangle_it 1.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.895 r_sphericity_free 29.397 r_dihedral_angle_4_deg 14.566 r_dihedral_angle_3_deg 10.956 r_sphericity_bonded 9.939 r_dihedral_angle_1_deg 8.697 r_long_range_B_refined 4.025 r_long_range_B_other 3.237 r_scangle_other 2.222 r_mcangle_it 1.854 r_mcangle_other 1.854 r_scbond_it 1.85 r_scbond_other 1.85 r_mcbond_it 1.512 r_mcbond_other 1.512 r_rigid_bond_restr 1.418 r_angle_refined_deg 1.353 r_angle_other_deg 0.935 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3313 Nucleic Acid Atoms Solvent Atoms 565 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing