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Structure of soluble SmhA crystal form 1 of the tripartite alpha-pore forming toxin, Smh, from Serratia marcescens.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 280 0.1 M MES pH 6.5, 0.16 M CaCl2 and 20 % PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.39 48.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.364 α = 90 b = 151.364 β = 90 c = 133.456 γ = 90
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 2019-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9792 Diamond I03
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 2.98 67.692 100 0.406 0.078 1 7.2 28.1 61518
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 2.98 3.03 3.048 0.575 0.6
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 SAD FREE R-VALUE 2.98 67.692 61482 3051 99.967 0.221 0.2196 0.2265 0.2539 0.2625 62.893
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] 1.356 1.356 -2.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.709 r_dihedral_angle_3_deg 14.519 r_dihedral_angle_4_deg 13.578 r_lrange_it 4.212 r_lrange_other 4.212 r_dihedral_angle_1_deg 3.273 r_mcangle_it 2.44 r_mcangle_other 2.44 r_scangle_it 2.263 r_scangle_other 2.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.709 r_dihedral_angle_3_deg 14.519 r_dihedral_angle_4_deg 13.578 r_lrange_it 4.212 r_lrange_other 4.212 r_dihedral_angle_1_deg 3.273 r_mcangle_it 2.44 r_mcangle_other 2.44 r_scangle_it 2.263 r_scangle_other 2.263 r_angle_refined_deg 1.627 r_mcbond_other 1.393 r_mcbond_it 1.392 r_scbond_it 1.355 r_scbond_other 1.355 r_angle_other_deg 1.305 r_symmetry_xyhbond_nbd_refined 0.361 r_nbd_other 0.253 r_symmetry_nbd_refined 0.231 r_nbd_refined 0.212 r_xyhbond_nbd_other 0.18 r_symmetry_nbd_other 0.169 r_nbtor_refined 0.154 r_xyhbond_nbd_refined 0.135 r_ncsr_local_group_22 0.114 r_ncsr_local_group_25 0.11 r_ncsr_local_group_7 0.109 r_ncsr_local_group_13 0.107 r_ncsr_local_group_18 0.106 r_ncsr_local_group_23 0.106 r_ncsr_local_group_28 0.106 r_ncsr_local_group_16 0.103 r_ncsr_local_group_14 0.102 r_ncsr_local_group_20 0.1 r_ncsr_local_group_5 0.099 r_ncsr_local_group_15 0.099 r_ncsr_local_group_27 0.099 r_ncsr_local_group_1 0.098 r_ncsr_local_group_17 0.098 r_ncsr_local_group_26 0.098 r_ncsr_local_group_10 0.096 r_ncsr_local_group_9 0.095 r_ncsr_local_group_12 0.095 r_ncsr_local_group_2 0.094 r_ncsr_local_group_8 0.094 r_ncsr_local_group_19 0.093 r_ncsr_local_group_21 0.092 r_ncsr_local_group_3 0.091 r_ncsr_local_group_6 0.087 r_ncsr_local_group_4 0.086 r_ncsr_local_group_11 0.086 r_ncsr_local_group_24 0.084 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_symmetry_xyhbond_nbd_other 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20420 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling CRANK phasing