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Crystal structure of the light chain of botulinum neurotoxin X (residues 2-427)
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 7.5 293 0.1M HEPES
10% w/v PEG 8000
8% v/v Ethylene glycol
pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.36 47.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.6 α = 90 b = 86.95 β = 90 c = 93.39 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 2018-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000041 SLS X06SA
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 1.308 43.11 99.75 0.07264 0.07565 0.02087 1 18.36 13.1 115320 17.89
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 1.308 1.355 98.24 2.878 2.996 0.8238 0.493 0.9 13
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 1.308 43.11 1.35 115280 5764 99.76 0.1503 0.1493 0.1516 0.169 0.1711
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 13.293 f_angle_d 0.949 f_chiral_restr 0.077 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3313 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing