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Crystal structure of the enzymatic component C2-I of the C2-toxin from Clostridium botulinum at pH 6.1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J3V PDB ENTRY 2J3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 PROTEIN: 14 MG/ML IN H2O RESERVOIR: 0.1 M MES PH 6.1, 2.1 M (NH4)2SO4, 0.03 M COCL2 HANGING DROP 1:1
Crystal Properties Matthews coefficient Solvent content 2.66 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.421 α = 90 b = 272.898 β = 90 c = 246.29 γ = 90
Symmetry Space Group C 2 2 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.26 91 92.8 0.04 23.7 4.3 136331 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.36 77.7 0.13 8.8
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 PDB ENTRY 2J3V 2.3 40 129810 2650 100 0.201 0.2 0.2005 0.258 0.2595 RANDOM 38.4
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] 3.73 -0.51 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_4_deg 20.429 r_dihedral_angle_3_deg 17.475 r_dihedral_angle_1_deg 6.343 r_scangle_it 2.194 r_angle_refined_deg 1.603 r_scbond_it 1.412 r_mcangle_it 0.899 r_mcbond_it 0.542 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_4_deg 20.429 r_dihedral_angle_3_deg 17.475 r_dihedral_angle_1_deg 6.343 r_scangle_it 2.194 r_angle_refined_deg 1.603 r_scbond_it 1.412 r_mcangle_it 0.899 r_mcbond_it 0.542 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.258 r_symmetry_hbond_refined 0.208 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20631 Nucleic Acid Atoms Solvent Atoms 592 Heterogen Atoms 279
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing