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Structure of the SmhB pore 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 6GRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 280.15 0.2M Calcium chloride, 40% MPD
Crystal Properties Matthews coefficient Solvent content 3.4 63.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 224.481 α = 90 b = 118.062 β = 109.438 c = 209.532 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2018-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9795 Diamond I24
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 6.979 66.769 98.8 2.295 1.403 0.7 1.3 3.5 28759 8304
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 6.979 7.1 3.384 2.356 0.5
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 6GRJ 6.979 66.769 8304 424 98.693 0.334 0.3341 0.3503 0.3351 0.3906 0.32
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] 8.38 5.016 29.781 -33.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.108 r_angle_other_deg 1.63 r_angle_refined_deg 1.496 r_symmetry_nbd_refined 0.427 r_nbd_refined 0.187 r_nbd_other 0.176 r_symmetry_nbd_other 0.154 r_nbtor_refined 0.102 r_symmetry_nbtor_other 0.087 r_ncsr_local_group_8 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.108 r_angle_other_deg 1.63 r_angle_refined_deg 1.496 r_symmetry_nbd_refined 0.427 r_nbd_refined 0.187 r_nbd_other 0.176 r_symmetry_nbd_other 0.154 r_nbtor_refined 0.102 r_symmetry_nbtor_other 0.087 r_ncsr_local_group_8 0.08 r_ncsr_local_group_34 0.079 r_ncsr_local_group_9 0.078 r_ncsr_local_group_23 0.078 r_ncsr_local_group_24 0.078 r_ncsr_local_group_41 0.078 r_ncsr_local_group_43 0.078 r_ncsr_local_group_5 0.077 r_ncsr_local_group_3 0.076 r_ncsr_local_group_20 0.076 r_ncsr_local_group_31 0.076 r_ncsr_local_group_1 0.075 r_ncsr_local_group_25 0.075 r_ncsr_local_group_28 0.075 r_ncsr_local_group_35 0.075 r_ncsr_local_group_42 0.075 r_ncsr_local_group_14 0.074 r_ncsr_local_group_18 0.074 r_ncsr_local_group_36 0.074 r_ncsr_local_group_44 0.074 r_ncsr_local_group_10 0.073 r_ncsr_local_group_12 0.073 r_ncsr_local_group_27 0.073 r_ncsr_local_group_15 0.072 r_ncsr_local_group_37 0.072 r_xyhbond_nbd_refined 0.066 r_ncsr_local_group_39 0.05 r_ncsr_local_group_13 0.049 r_ncsr_local_group_26 0.047 r_ncsr_local_group_38 0.045 r_ncsr_local_group_29 0.042 r_ncsr_local_group_45 0.041 r_ncsr_local_group_16 0.04 r_ncsr_local_group_17 0.031 r_chiral_restr 0.025 r_ncsr_local_group_6 0.024 r_ncsr_local_group_21 0.023 r_ncsr_local_group_7 0.022 r_ncsr_local_group_4 0.021 r_ncsr_local_group_19 0.019 r_ncsr_local_group_22 0.019 r_ncsr_local_group_11 0.018 r_ncsr_local_group_32 0.017 r_ncsr_local_group_2 0.016 r_ncsr_local_group_40 0.015 r_ncsr_local_group_33 0.013 r_ncsr_local_group_30 0.009 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_lrange_it r_lrange_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15778 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing