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SufS from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.35 293 Tris, ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.77 55.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.853 α = 90 b = 93.853 β = 90 c = 101.461 γ = 120
Symmetry Space Group P 32 2 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 Bruker PHOTON III Helios MX 2021-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.34
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.388 31.737 100 0.015 0.021 0.015 22.8 22.6 104403
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.388 1.41 97.6 0.415 0.587 0.415 2.1 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5J8Q 1.388 31.737 104344 2054 99.863 0.168 0.1679 0.1776 0.1911 0.2015 17.802
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] -0.098 -0.049 -0.098 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.996 r_dihedral_angle_4_deg 15.871 r_dihedral_angle_3_deg 11.757 r_dihedral_angle_1_deg 6.148 r_lrange_it 4.952 r_lrange_other 4.85 r_scangle_it 4.359 r_scangle_other 4.358 r_scbond_it 2.96 r_scbond_other 2.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.996 r_dihedral_angle_4_deg 15.871 r_dihedral_angle_3_deg 11.757 r_dihedral_angle_1_deg 6.148 r_lrange_it 4.952 r_lrange_other 4.85 r_scangle_it 4.359 r_scangle_other 4.358 r_scbond_it 2.96 r_scbond_other 2.959 r_angle_refined_deg 2.054 r_angle_other_deg 2.023 r_mcangle_other 1.924 r_mcangle_it 1.92 r_mcbond_it 1.403 r_mcbond_other 1.392 r_nbd_refined 0.241 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.177 r_nbd_other 0.151 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.085 r_xyhbond_nbd_other 0.078 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3272 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement APEX data reduction APEX data scaling PHASER phasing