☰ Navigation Tabs
Structure of soluble SmhB 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 6GRK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 280.15 0.17 M ammonium sulphate, 25.5 % PEG4000
Crystal Properties Matthews coefficient Solvent content 2.46 49.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.94 α = 90 b = 113.95 β = 90 c = 130.37 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 PILATUS 6M-F 2018-09-03 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 1.84 65.185 99.8 0.139 0.078 1 9.5 6.7 66582
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 1.84 1.87 1.214 0.842 0.5 1
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 6GRK 1.84 65.185 66506 3268 99.661 0.189 0.1872 0.1879 0.224 0.225 24.839
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] -0.509 -1.266 1.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.939 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 13.555 r_lrange_it 8.513 r_lrange_other 8.512 r_scangle_it 8.001 r_scangle_other 8 r_scbond_it 6.34 r_scbond_other 6.34 r_dihedral_angle_1_deg 4.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.939 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 13.555 r_lrange_it 8.513 r_lrange_other 8.512 r_scangle_it 8.001 r_scangle_other 8 r_scbond_it 6.34 r_scbond_other 6.34 r_dihedral_angle_1_deg 4.972 r_mcangle_other 3.596 r_mcangle_it 3.592 r_mcbond_it 3.13 r_mcbond_other 3.115 r_angle_refined_deg 1.759 r_angle_other_deg 1.542 r_symmetry_nbd_refined 0.391 r_symmetry_xyhbond_nbd_refined 0.329 r_nbd_refined 0.217 r_nbd_other 0.192 r_symmetry_nbd_other 0.173 r_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.161 r_ncsr_local_group_1 0.142 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5389 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing