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Structure of soluble SmhA 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 7A26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 280 0.2M potassium nitrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.59 52.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.24 α = 90 b = 92.58 β = 90 c = 221.1 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 80 PIXEL DECTRIS EIGER2 XE 16M 2019-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9159 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.57 110.55 99.9 0.19 0.055 1 8.5 13 53914
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 2.57 2.61 2.129 0.595 0.8
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 7A26 2.57 110.55 53847 2611 99.75 0.236 0.2357 0.2358 0.247 0.2471 72.64
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] -1.09 10.982 -9.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.996 r_dihedral_angle_3_deg 14.581 r_dihedral_angle_4_deg 13.544 r_lrange_it 3.584 r_lrange_other 3.567 r_dihedral_angle_1_deg 3.253 r_mcangle_it 2.287 r_mcangle_other 2.287 r_scangle_it 2.1 r_scangle_other 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.996 r_dihedral_angle_3_deg 14.581 r_dihedral_angle_4_deg 13.544 r_lrange_it 3.584 r_lrange_other 3.567 r_dihedral_angle_1_deg 3.253 r_mcangle_it 2.287 r_mcangle_other 2.287 r_scangle_it 2.1 r_scangle_other 2.1 r_angle_refined_deg 1.555 r_mcbond_it 1.345 r_mcbond_other 1.345 r_angle_other_deg 1.295 r_scbond_it 1.214 r_scbond_other 1.213 r_symmetry_nbd_refined 0.212 r_nbd_refined 0.204 r_nbd_other 0.195 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.149 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.094 r_ncsr_local_group_1 0.094 r_ncsr_local_group_4 0.093 r_ncsr_local_group_3 0.091 r_ncsr_local_group_6 0.089 r_ncsr_local_group_5 0.087 r_ncsr_local_group_2 0.085 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.076 r_bond_refined_d 0.007 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 10372 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing