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Crystal structure of the progenitor M complex of Clostridium botulinum type E neurotoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FFZ 3FFZ, 3V0A experimental model PDB 3V0A 3FFZ, 3V0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 294 5.0ul sample was equilibrated against 600ul of 6 - 8% PEG 4000 and 0.1M sodium acetate of pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.77 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.601 α = 90 b = 192.601 β = 90 c = 286.538 γ = 120
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 315 2013-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3 50 69.8 2.3 4.5 165586 110.6
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 3FFZ, 3V0A 3.05 49.3 133607 1334 59.72 0.24415 0.24338 0.2472 0.32083 0.3144 RANDOM 134.999
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] 1.03 1.03 1.03 -3.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.42 r_long_range_B_refined 30.731 r_long_range_B_other 30.731 r_scangle_other 21.831 r_mcangle_it 19.914 r_mcangle_other 19.914 r_dihedral_angle_3_deg 18.734 r_dihedral_angle_4_deg 17.001 r_scbond_it 12.958 r_scbond_other 12.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.42 r_long_range_B_refined 30.731 r_long_range_B_other 30.731 r_scangle_other 21.831 r_mcangle_it 19.914 r_mcangle_other 19.914 r_dihedral_angle_3_deg 18.734 r_dihedral_angle_4_deg 17.001 r_scbond_it 12.958 r_scbond_other 12.957 r_mcbond_it 12.49 r_mcbond_other 12.488 r_dihedral_angle_1_deg 7.841 r_angle_refined_deg 1.438 r_angle_other_deg 0.94 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 56949 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing