☰ Navigation Tabs
Crystal structure of the LHn fragment of botulinum neurotoxin type D, mutant H233Y E230Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289.1 30 % v/v pentaerythritol ethoxylate (15/4 EO/OH), 0.1 M HEPES 7.5, 6 % w/v polyvinylpyrrolidone
Crystal Properties Matthews coefficient Solvent content 4.8 74.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.545 α = 90 b = 173.545 β = 90 c = 222.191 γ = 120
Symmetry Space Group P 64 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 PIXEL DECTRIS PILATUS 6M 2014-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 2.3 150 98.8 0.049 13 3.7 86306 86306
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 2.3 2.34 97.7 1.09 0.5 2.6
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 2FPQ 2.3 150 82020 4277 98.4 0.22144 0.22015 0.2249 0.2467 0.2499 RANDOM 77.043
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] 0.48 0.24 0.48 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.75 r_dihedral_angle_4_deg 16.634 r_dihedral_angle_3_deg 15.657 r_long_range_B_refined 7.199 r_long_range_B_other 7.185 r_dihedral_angle_1_deg 7.085 r_scangle_other 4.513 r_mcangle_it 4.34 r_mcangle_other 4.339 r_scbond_it 2.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.75 r_dihedral_angle_4_deg 16.634 r_dihedral_angle_3_deg 15.657 r_long_range_B_refined 7.199 r_long_range_B_other 7.185 r_dihedral_angle_1_deg 7.085 r_scangle_other 4.513 r_mcangle_it 4.34 r_mcangle_other 4.339 r_scbond_it 2.666 r_scbond_other 2.665 r_mcbond_it 2.602 r_mcbond_other 2.593 r_angle_refined_deg 1.517 r_angle_other_deg 0.975 r_chiral_restr 0.109 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 6690 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing