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Simkania negevensis CE-clan virulence factor SnCE1 C256A catalytically inactive mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-F8L4W9-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.6 M sodium chloride, 0.1 M MES pH 6.5, 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.05 39.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.626 α = 90 b = 151.173 β = 105.073 c = 80.777 γ = 90
Symmetry Space Group P 1 21 1
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 2022-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.8856 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 2.2 48.55 96 0.108 0.128 0.067 0.998 9.7 6.9 87960 38.8
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 2.2 2.24 44.3 1.715 2.248 1.428 0.309 0.6 3.5
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 2.205 48.55 87925 4202 95.992 0.157 0.155 0.154 0.1906 0.1891 50.905
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] -0.527 -2.927 0.372 1.512
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.544 r_dihedral_angle_3_deg 16.241 r_dihedral_angle_4_deg 15.642 r_dihedral_angle_1_deg 6.968 r_lrange_it 6.927 r_lrange_other 6.899 r_scangle_it 4.627 r_scangle_other 4.627 r_mcangle_it 3.03 r_mcangle_other 3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.544 r_dihedral_angle_3_deg 16.241 r_dihedral_angle_4_deg 15.642 r_dihedral_angle_1_deg 6.968 r_lrange_it 6.927 r_lrange_other 6.899 r_scangle_it 4.627 r_scangle_other 4.627 r_mcangle_it 3.03 r_mcangle_other 3.03 r_scbond_it 2.913 r_scbond_other 2.912 r_mcbond_it 2.079 r_mcbond_other 2.079 r_angle_refined_deg 1.636 r_angle_other_deg 1.312 r_nbd_other 0.224 r_nbd_refined 0.197 r_symmetry_xyhbond_nbd_refined 0.181 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.172 r_xyhbond_nbd_refined 0.159 r_metal_ion_refined 0.09 r_ncsr_local_group_2 0.087 r_ncsr_local_group_17 0.086 r_ncsr_local_group_24 0.084 r_ncsr_local_group_21 0.083 r_chiral_restr 0.082 r_ncsr_local_group_14 0.082 r_ncsr_local_group_15 0.082 r_ncsr_local_group_9 0.081 r_ncsr_local_group_12 0.08 r_ncsr_local_group_4 0.079 r_ncsr_local_group_23 0.079 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_20 0.078 r_ncsr_local_group_5 0.077 r_ncsr_local_group_26 0.077 r_ncsr_local_group_18 0.076 r_ncsr_local_group_28 0.076 r_ncsr_local_group_1 0.075 r_ncsr_local_group_3 0.075 r_ncsr_local_group_16 0.075 r_ncsr_local_group_6 0.074 r_ncsr_local_group_8 0.074 r_ncsr_local_group_10 0.074 r_ncsr_local_group_11 0.073 r_ncsr_local_group_22 0.073 r_ncsr_local_group_13 0.071 r_ncsr_local_group_27 0.071 r_ncsr_local_group_25 0.068 r_ncsr_local_group_7 0.065 r_ncsr_local_group_19 0.063 r_bond_refined_d 0.011 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 13519 Nucleic Acid Atoms Solvent Atoms 881 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing XDS data reduction XDS data scaling MxCuBE data collection