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Simkania negevensis CE-clan virulence factor SnCE1 in complex with hsSUMO1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other D_1292146185 experimental model PDB 4WJQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M calcium acetate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.95 37.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.967 α = 90 b = 56.164 β = 90 c = 148.651 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 100 PIXEL DECTRIS PILATUS3 S 6M 2025-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.55 49.55 100 0.117 0.127 0.049 0.999 11.9 12.6 43672 22.96
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 1.55 1.58 100 1.397 1.532 0.624 0.352 1.7 11.4
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 1.55 37.19 43575 2250 99.938 0.157 0.1534 0.1563 0.2163 0.2163 29.865
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] 2.018 -0.068 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.986 r_dihedral_angle_4_deg 15.469 r_dihedral_angle_3_deg 14.534 r_dihedral_angle_other_2_deg 10.01 r_dihedral_angle_1_deg 7.576 r_scangle_it 4.828 r_scangle_other 4.827 r_lrange_it 4.671 r_lrange_other 4.628 r_scbond_it 4.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.986 r_dihedral_angle_4_deg 15.469 r_dihedral_angle_3_deg 14.534 r_dihedral_angle_other_2_deg 10.01 r_dihedral_angle_1_deg 7.576 r_scangle_it 4.828 r_scangle_other 4.827 r_lrange_it 4.671 r_lrange_other 4.628 r_scbond_it 4.165 r_scbond_other 4.163 r_mcangle_it 3.692 r_mcangle_other 3.692 r_rigid_bond_restr 3.68 r_mcbond_other 3.225 r_mcbond_it 3.223 r_angle_refined_deg 1.748 r_angle_other_deg 1.442 r_dihedral_angle_other_3_deg 0.585 r_nbd_other 0.264 r_nbd_refined 0.237 r_symmetry_nbd_refined 0.215 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.142 r_metal_ion_refined 0.099 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.082 r_symmetry_metal_ion_refined 0.044 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2355 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building PHASER phasing XDS data reduction XDS data scaling MxCuBE data collection