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Crystal structure of HA33A, a neurotoxin-associated protein from Clostridium botulinum type A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QXM pdb entry 1QXM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG 4000, 15% isopropanol, 200 mM Li2SO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.084 α = 90 b = 146.595 β = 90 c = 35.712 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.9179 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.5 25 87 0.066 13.6 88654 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.539 78.6 0.299 3.7 88654
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1QXM 1.5 21.22 1 73397 3820 87.09 0.16904 0.16771 0.19445 0.277 RANDOM 19.526
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.222 r_dihedral_angle_4_deg 15.771 r_dihedral_angle_3_deg 11.572 r_dihedral_angle_1_deg 7.273 r_scangle_it 2.563 r_scbond_it 1.863 r_angle_refined_deg 1.239 r_mcangle_it 1.068 r_mcbond_it 0.858 r_angle_other_deg 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.222 r_dihedral_angle_4_deg 15.771 r_dihedral_angle_3_deg 11.572 r_dihedral_angle_1_deg 7.273 r_scangle_it 2.563 r_scbond_it 1.863 r_angle_refined_deg 1.239 r_mcangle_it 1.068 r_mcbond_it 0.858 r_angle_other_deg 0.74 r_symmetry_vdw_other 0.272 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.217 r_nbd_other 0.189 r_nbtor_refined 0.18 r_mcbond_other 0.165 r_symmetry_hbond_refined 0.139 r_xyhbond_nbd_refined 0.135 r_nbtor_other 0.083 r_chiral_restr 0.078 r_xyhbond_nbd_other 0.024 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4677 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement