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Crystal structure of the enzymatic component C2-I of the C2-toxin from Clostridium botulinum at pH 3.0 (mut-S361R)
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 3 PROTEIN: 10 MG/ML RESERVOIR: 0.1 M CITRAT PH 3.0, 0.8 M (NH4)2SO4 HANGING DROP 1:1
Crystal Properties Matthews coefficient Solvent content 3.15 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.72 α = 90 b = 115.72 β = 90 c = 162.83 γ = 120
Symmetry Space Group P 63 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.75 48 96.6 0.07 23.6 7.4 63100 -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 1.75 1.82 94.3 0.45 3.1
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 1.75 47.14 60575 2523 100 0.169 0.168 0.1686 0.197 0.1976 RANDOM 20.71
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] 0.33 0.17 0.33 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.476 r_dihedral_angle_4_deg 21.008 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_1_deg 5.922 r_scangle_it 4.494 r_scbond_it 2.918 r_mcangle_it 2.011 r_angle_refined_deg 1.78 r_mcbond_it 1.279 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.476 r_dihedral_angle_4_deg 21.008 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_1_deg 5.922 r_scangle_it 4.494 r_scbond_it 2.918 r_mcangle_it 2.011 r_angle_refined_deg 1.78 r_mcbond_it 1.279 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.216 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.15 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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 3479 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling