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Crystal structure of BoNT/A-LCHn domain in complex with VHH ciA-D12, ciA-B5, and ciA-H7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 291 11 % PEG 20,000 and 0.1 M sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.91 57.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.04 α = 90 b = 89.36 β = 118.93 c = 143.69 γ = 90
Symmetry Space Group C 1 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 CCD ADSC QUANTUM 315r 2014-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.12709 SSRL BL7-1
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 2.2 37.74 95 0.049 0.069 0.049 0.997 10.2 2.6 75271 29.5981913921
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 2.2 2.25 0.208 0.207 0.965
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 3V0A 2.20000858936 37.1635590417 1.33647799258 75238 3774 94.7832550171 0.182987256077 0.180585060409 0.1832 0.228599973817 0.2289 34.9171563415
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 13.8050176631 f_angle_d 1.08750663266 f_chiral_restr 0.0459275854207 f_bond_d 0.00848919676619 f_plane_restr 0.00471204337883
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9564 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement Blu-Ice data collection SCALA data scaling PHASER phasing XDS data reduction