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Structure of soluble SmhB crystal form 2 of the tripartite alpha-pore forming toxin, Smh, from Serratia marcescens.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 280.15 0.22M Magnesium chloride hexahydrate
0.1M Na acetate pH 5.15, 26% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.65 53.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.931 α = 90 b = 49.729 β = 118.427 c = 99.495 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M-F 2020-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.86 87.51 90.2 0.1 0.044 0.8 10.4 10.4 50442
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.88 0.899 0.525 0.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ZZ5 1.86 87.498 50442 2521 72.222 0.215 0.2133 0.2099 0.2471 0.2449 29.312
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] -0.76 0.738 0.026 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.989 r_dihedral_angle_4_deg 14.346 r_dihedral_angle_3_deg 13.231 r_lrange_it 6.225 r_lrange_other 6.217 r_scangle_it 4.568 r_scangle_other 4.568 r_dihedral_angle_1_deg 3.667 r_mcangle_it 2.967 r_mcangle_other 2.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.989 r_dihedral_angle_4_deg 14.346 r_dihedral_angle_3_deg 13.231 r_lrange_it 6.225 r_lrange_other 6.217 r_scangle_it 4.568 r_scangle_other 4.568 r_dihedral_angle_1_deg 3.667 r_mcangle_it 2.967 r_mcangle_other 2.966 r_scbond_it 2.937 r_scbond_other 2.936 r_mcbond_it 1.931 r_mcbond_other 1.929 r_angle_refined_deg 1.656 r_angle_other_deg 1.513 r_symmetry_xyhbond_nbd_other 0.279 r_nbd_other 0.265 r_symmetry_nbd_refined 0.252 r_nbd_refined 0.226 r_symmetry_xyhbond_nbd_refined 0.196 r_xyhbond_nbd_refined 0.188 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.164 r_ncsr_local_group_1 0.122 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5426 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement STARANISO data reduction STARANISO data scaling PHASER phasing