☰ Navigation Tabs
Crystal structure of mutant exfoliative toxin C (ExhC) from Mammaliicoccus sciuri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.2 M MgCl2; 0.1 M Tris-HCl pH 8.5 and 30% w/v PEG 4000 with the addition of 0.1 M Sarcosine
Crystal Properties Matthews coefficient Solvent content 2.02 38.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.15 α = 90 b = 71.398 β = 94.705 c = 71.383 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 PILATUS 2M 2020-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 1.323630 LNLS SIRIUS MANACA
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 1.57 39.553 99.9 0.06174 0.02589 0.999 15.17 6.5 63061
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 1.57 1.626 0.06174 0.5632 0.506 1.14
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 1.57 39.553 63061 3153 99.894 0.183 0.1813 0.1815 0.2229 0.2233 27.023
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] -1.512 0.232 1.167 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.779 r_dihedral_angle_3_deg 14.362 r_lrange_other 8.385 r_lrange_it 8.378 r_scangle_it 7.415 r_scangle_other 7.413 r_dihedral_angle_1_deg 7.158 r_dihedral_angle_2_deg 6.904 r_scbond_it 5.124 r_scbond_other 5.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.779 r_dihedral_angle_3_deg 14.362 r_lrange_other 8.385 r_lrange_it 8.378 r_scangle_it 7.415 r_scangle_other 7.413 r_dihedral_angle_1_deg 7.158 r_dihedral_angle_2_deg 6.904 r_scbond_it 5.124 r_scbond_other 5.123 r_mcangle_other 4.351 r_mcangle_it 4.35 r_mcbond_it 3.336 r_mcbond_other 3.336 r_angle_refined_deg 2.152 r_angle_other_deg 0.699 r_nbd_refined 0.213 r_symmetry_xyhbond_nbd_refined 0.212 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.187 r_nbd_other 0.137 r_symmetry_nbd_refined 0.12 r_chiral_restr 0.107 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_symmetry_xyhbond_nbd_other 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 3711 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing