☰ Navigation Tabs
Pseudomonas exotoxin A domain III T18H477L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XK9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.66 M sodium citrate pH 7.5, 0.54 mM sodium azide, 0.3 mM dithiothreitol, 0.5 mM PJ34
1.1 M sodium citrate pH 7.5, 0.9 mM sodium azide, 0.5 mM dithiothreitol 0.5 mM PJ34
Crystal Properties Matthews coefficient Solvent content 2.01 38.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.373 α = 90 b = 48.188 β = 90 c = 99.002 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2017-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.03320 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.47 49.5 99.4 0.067 0.999 16.51 8.24 32473
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.54 96.9 0.959 0.805 2.14 7.76
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 1XK9 1.47 49.5 30481 1549 99.94 0.1781 0.17742 0.1782 0.19195 0.1923 RANDOM 28.335
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] 0.26 -1.31 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.416 r_dihedral_angle_4_deg 16.998 r_dihedral_angle_3_deg 11.816 r_long_range_B_other 8.863 r_long_range_B_refined 8.844 r_scangle_other 6.735 r_dihedral_angle_1_deg 5.683 r_mcangle_it 4.779 r_mcangle_other 4.775 r_scbond_it 4.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.416 r_dihedral_angle_4_deg 16.998 r_dihedral_angle_3_deg 11.816 r_long_range_B_other 8.863 r_long_range_B_refined 8.844 r_scangle_other 6.735 r_dihedral_angle_1_deg 5.683 r_mcangle_it 4.779 r_mcangle_other 4.775 r_scbond_it 4.482 r_scbond_other 4.48 r_mcbond_it 3.17 r_mcbond_other 3.132 r_angle_refined_deg 2.439 r_angle_other_deg 1.273 r_chiral_restr 0.173 r_bond_refined_d 0.027 r_gen_planes_refined 0.015 r_gen_planes_other 0.005 r_bond_other_d 0.002 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 1608 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing