☰ Navigation Tabs
Clostridium botulinum Hemagglutinin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E4M PDB ENTRY 2E4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 0.25M ammonium chloride, 3%(w/v) polyethylene glycol 4000, 3% trehalose, 3%(w/v) benzamidine HCl, 3%(w/v) methylpentanediol, 3%(w/v) ethylene glycol, 0.1M calcium chloride, 0.1M Tris-HCl , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 5.51 77.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 324.726 α = 90 b = 324.726 β = 90 c = 117.588 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 RAYONIX MX300HE 2013-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 3.5 50 98.3 0.054 3.5 45595 1 1 83.2
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 3.5 3.63 98.4 0.494 3.2 4478
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2E4M 3.5 48.43 45595 43265 2323 98.25 0.2025 0.19992 0.1989 0.2512 0.1961 RANDOM 113.213
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] 0.03 0.03 0.03 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.855 r_dihedral_angle_3_deg 21.361 r_dihedral_angle_4_deg 18.206 r_long_range_B_refined 12.265 r_long_range_B_other 12.263 r_dihedral_angle_1_deg 9.041 r_scangle_other 8.624 r_mcangle_it 8.311 r_mcangle_other 8.31 r_scbond_it 5.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.855 r_dihedral_angle_3_deg 21.361 r_dihedral_angle_4_deg 18.206 r_long_range_B_refined 12.265 r_long_range_B_other 12.263 r_dihedral_angle_1_deg 9.041 r_scangle_other 8.624 r_mcangle_it 8.311 r_mcangle_other 8.31 r_scbond_it 5.342 r_scbond_other 5.342 r_mcbond_it 5.197 r_mcbond_other 5.197 r_angle_refined_deg 1.648 r_angle_other_deg 0.894 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10472 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling