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Crystal structure of native exfoliative toxin C (ExhC) from Mammaliicoccus sciuri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8T3I ExhC mutant (R47A, N49F, Q51K and R89A)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1 M HEPES pH 7.5 and 0.8 M Potassium/Sodium tartrate
Crystal Properties Matthews coefficient Solvent content 3.21 61.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.094 α = 90 b = 167.094 β = 90 c = 157.743 γ = 90
Symmetry Space Group I 4 2 2
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 PILATUS 2M 2021-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.977180 LNLS SIRIUS MANACA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.705 47.283 99.92 0.06747 0.995 8.4 26.2 30672
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.71 2.807 0.7518 0.45 0.79
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 2.705 47.283 30672 1534 99.808 0.214 0.2113 0.2124 0.2701 0.2688 80.759
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] -1.437 -1.437 2.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.198 r_dihedral_angle_6_deg 15.24 r_lrange_other 13.186 r_lrange_it 13.184 r_dihedral_angle_2_deg 11.786 r_scangle_it 10.058 r_scangle_other 10.056 r_mcangle_it 9.2 r_mcangle_other 9.2 r_dihedral_angle_1_deg 7.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.198 r_dihedral_angle_6_deg 15.24 r_lrange_other 13.186 r_lrange_it 13.184 r_dihedral_angle_2_deg 11.786 r_scangle_it 10.058 r_scangle_other 10.056 r_mcangle_it 9.2 r_mcangle_other 9.2 r_dihedral_angle_1_deg 7.83 r_scbond_it 6.631 r_scbond_other 6.629 r_mcbond_it 6.117 r_mcbond_other 6.117 r_angle_refined_deg 1.546 r_angle_other_deg 0.517 r_symmetry_xyhbond_nbd_refined 0.261 r_nbd_refined 0.218 r_symmetry_nbd_other 0.209 r_nbd_other 0.193 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.181 r_symmetry_nbd_refined 0.165 r_symmetry_xyhbond_nbd_other 0.129 r_ncsr_local_group_2 0.106 r_ncsr_local_group_3 0.097 r_ncsr_local_group_1 0.095 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5502 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing