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Structure of a functional derivative of Clostridium botulinum neurotoxin type B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EPW PDB ENTRY 1EPW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.2 15% PEG3350, 0.1M BIS-TRIS-PROPANE PH 6.5, 0.2M SODIUM SULPHATE
Crystal Properties Matthews coefficient Solvent content 2.8 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.89 α = 90 b = 149.1 β = 90 c = 113.49 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315 MIRRORS 2010-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.8 37.64 99.8 0.12 10.3 5.8 28644
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 2.8 2.95 100 0.51 3.5 5.8
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 1EPW 2.8 113.49 27162 1448 99.69 0.24213 0.23999 0.2308 0.28231 0.2453 RANDOM 36.557
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] -3.06 0.48 2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.817 r_dihedral_angle_3_deg 13.921 r_dihedral_angle_4_deg 13.914 r_dihedral_angle_1_deg 4.371 r_scangle_it 1.017 r_angle_refined_deg 0.855 r_mcangle_it 0.57 r_scbond_it 0.558 r_mcbond_it 0.304 r_chiral_restr 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.817 r_dihedral_angle_3_deg 13.921 r_dihedral_angle_4_deg 13.914 r_dihedral_angle_1_deg 4.371 r_scangle_it 1.017 r_angle_refined_deg 0.855 r_mcangle_it 0.57 r_scbond_it 0.558 r_mcbond_it 0.304 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 6828 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing