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Crystal structure of Shewanella putrefaciens PE-like toxin, Spx
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294.15 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000 (condition C10 of the PACT premier Screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.65 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.196 α = 90 b = 121.196 β = 90 c = 125.216 γ = 120
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 EIGER2 XE 16M 2021-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.79 104.83 100 0.28 0.287 0.062 0.997 7.5 21.5 193517
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.82 99.7 3.695 3.784 0.811 0.339 0.4 21.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.861 104.83 172116 8476 99.694 0.187 0.185 0.1837 0.2204 0.2202 34.028
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] 0.486 0.243 0.486 -1.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.939 r_dihedral_angle_4_deg 15.838 r_dihedral_angle_3_deg 11.536 r_dihedral_angle_1_deg 6.731 r_lrange_it 5.49 r_lrange_other 5.44 r_scangle_it 3.686 r_scangle_other 3.686 r_mcangle_it 2.876 r_mcangle_other 2.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.939 r_dihedral_angle_4_deg 15.838 r_dihedral_angle_3_deg 11.536 r_dihedral_angle_1_deg 6.731 r_lrange_it 5.49 r_lrange_other 5.44 r_scangle_it 3.686 r_scangle_other 3.686 r_mcangle_it 2.876 r_mcangle_other 2.876 r_scbond_it 2.247 r_scbond_other 2.246 r_mcbond_it 1.79 r_mcbond_other 1.789 r_angle_refined_deg 1.283 r_angle_other_deg 1.221 r_metal_ion_refined 0.255 r_symmetry_nbd_refined 0.245 r_nbd_refined 0.19 r_symmetry_nbd_other 0.179 r_nbd_other 0.176 r_nbtor_refined 0.152 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_other 0.079 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.053 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13905 Nucleic Acid Atoms Solvent Atoms 1241 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing