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Crystal Structure of Botulinum Neurotoxin Type G Light Chain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F82 PDB ENTRY 1F82
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 6.00% PEG 6000, 0.65M Lithium Chloride, 0.10M Sodium Citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.5 64.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.866 α = 90 b = 178.866 β = 90 c = 80.864 γ = 120
Symmetry Space Group P 62 2 2
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 MARMOSAIC 225 mm CCD 2004-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.00863 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.35 50 93.9 0.053 24.4 7.5 30233 30233 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.411 95.3 0.395 4.8 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1F82 2.35 24.81 28690 28690 1536 93.97 0.17612 0.17364 0.17364 0.2154 0.22216 0.2581 RANDOM 43.78
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] 0.09 0.04 0.09 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.966 r_dihedral_angle_4_deg 22.863 r_dihedral_angle_3_deg 17.414 r_dihedral_angle_1_deg 7.782 r_scangle_it 5.253 r_scbond_it 3.588 r_mcangle_it 2.283 r_angle_refined_deg 2.031 r_mcbond_it 1.831 r_angle_other_deg 1.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.966 r_dihedral_angle_4_deg 22.863 r_dihedral_angle_3_deg 17.414 r_dihedral_angle_1_deg 7.782 r_scangle_it 5.253 r_scbond_it 3.588 r_mcangle_it 2.283 r_angle_refined_deg 2.031 r_mcbond_it 1.831 r_angle_other_deg 1.046 r_symmetry_vdw_refined 0.375 r_mcbond_other 0.3 r_symmetry_vdw_other 0.25 r_symmetry_hbond_refined 0.235 r_metal_ion_refined 0.23 r_nbd_refined 0.214 r_nbd_other 0.203 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.132 r_nbtor_other 0.096 r_bond_refined_d 0.027 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3322 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement