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Crystal structure of the light chain of botulinum neurotoxin X (residues 2-442)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1M HEPES
10% w/v PEG 6000
pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.32 α = 90 b = 87.26 β = 90 c = 93.85 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 EIGER X 16M 2017-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999998 SLS X06DA
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 1.45 41.328 99.86 0.07576 0.07888 0.02165 0.999 18.51 13.3 88274 22.65
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 1.45 1.502 99.89 2.994 3.111 0.8365 0.424 0.9 13.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3QIZ 1.45 41.328 1.33 88257 4414 99.87 0.1457 0.1438 0.1468 0.1824 0.1845
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.236 f_angle_d 0.891 f_chiral_restr 0.08 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3391 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing