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Crystal structure of cysteine desulfurase SufS R376A from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZS9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M Tris-HCl, 50 mM Lithium sulfate, 50%(v/v) PEG200
Crystal Properties Matthews coefficient Solvent content 3.39 63.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.5 α = 90 b = 92.5 β = 90 c = 128.4 γ = 120
Symmetry Space Group P 31 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 DECTRIS PILATUS3 S 6M 2019-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.67 46.29 100 0.074 0.076 1 32.22 19.839 18572 71.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.67 2.77 99.9 0.937 0.96 0.895 3.44 20.562
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ZS9 2.67 46.29 17643 929 99.96 0.1748 0.1721 0.172 0.2269 0.2268 RANDOM 70.73
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] 0.14 0.07 0.14 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.388 r_dihedral_angle_4_deg 19.146 r_dihedral_angle_3_deg 17.401 r_dihedral_angle_1_deg 6.551 r_angle_refined_deg 1.934 r_chiral_restr 0.136 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3214 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 7
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing