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Simkania negevensis CE-clan virulence factor SnCE1 wildtype
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other D_1292146185
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.18 M sodium malonate pH 5.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.645 α = 90 b = 105.645 β = 90 c = 122.086 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 EIGER X 16M 2024-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.82 47.27 98.4 0.228 0.247 0.095 0.992 8.9 12.9 15908 48.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.82 2.97 89.1 0.941 1.073 0.497 0.569 2 7.5
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.821 44.1 15887 749 98.256 0.248 0.2467 0.2461 0.2687 0.2676 59.341
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] -1.681 -1.681 3.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.437 r_dihedral_angle_3_deg 16.869 r_dihedral_angle_4_deg 15.962 r_lrange_it 7.577 r_lrange_other 7.577 r_dihedral_angle_1_deg 6.926 r_mcangle_it 3.256 r_mcangle_other 3.255 r_scangle_it 3.002 r_scangle_other 3.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.437 r_dihedral_angle_3_deg 16.869 r_dihedral_angle_4_deg 15.962 r_lrange_it 7.577 r_lrange_other 7.577 r_dihedral_angle_1_deg 6.926 r_mcangle_it 3.256 r_mcangle_other 3.255 r_scangle_it 3.002 r_scangle_other 3.002 r_mcbond_it 1.992 r_mcbond_other 1.992 r_scbond_it 1.774 r_scbond_other 1.773 r_angle_refined_deg 1.572 r_angle_other_deg 1.287 r_symmetry_xyhbond_nbd_refined 0.465 r_ext_dist_refined_d 0.263 r_nbd_other 0.248 r_symmetry_nbd_refined 0.233 r_nbd_refined 0.193 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.175 r_xyhbond_nbd_other 0.126 r_xyhbond_nbd_refined 0.124 r_ncsr_local_group_3 0.089 r_ncsr_local_group_2 0.085 r_ncsr_local_group_1 0.082 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5057 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing XDS data reduction XDS data scaling MxCuBE data collection