☰ Navigation Tabs
Crystal structures reveal a thiol-protease like catalytic triad in the C-terminal region of Pasteurella multocida toxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EBF PDB ENTRY 2EBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 15% PEG 6000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.91 57.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.357 α = 90 b = 132.823 β = 114.74 c = 82.546 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MACSCIENCE mirrors 2006-07-03 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 2.6 50 97.2 0.094 3.6 59945 57847
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 2.6 2.69 88.5 0.473 3
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 2EBF 2.6 44.81 57615 54694 2921 97.01 0.23491 0.23217 0.2299 0.28632 0.2837 RANDOM 57.394
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 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.799 r_dihedral_angle_4_deg 19.228 r_dihedral_angle_3_deg 18.812 r_dihedral_angle_1_deg 5.768 r_scangle_it 1.27 r_angle_refined_deg 1.208 r_scbond_it 0.783 r_mcangle_it 0.739 r_mcbond_it 0.413 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.799 r_dihedral_angle_4_deg 19.228 r_dihedral_angle_3_deg 18.812 r_dihedral_angle_1_deg 5.768 r_scangle_it 1.27 r_angle_refined_deg 1.208 r_scbond_it 0.783 r_mcangle_it 0.739 r_mcbond_it 0.413 r_nbtor_refined 0.305 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11286 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing