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Crystal Structure of the Cysteine Desulfurase SufS of Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES pH 7.5,
50 % (v/v) PEG 400
Crystal Properties Matthews coefficient Solvent content 3.56 65.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.191 α = 90 b = 93.191 β = 90 c = 130.543 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 PILATUS 6M 2014-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.972 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.702 46.6 97 0.07071 2.7 9.4 72121
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.702 1.762
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4W91 1.702 46.6 68544 3577 99.6 0.11771 0.11612 0.14789 0.1654 RANDOM 29.428
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] 0.04 0.02 0.04 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.461 r_sphericity_free 34.795 r_dihedral_angle_4_deg 16.934 r_dihedral_angle_3_deg 12.664 r_sphericity_bonded 12.302 r_dihedral_angle_1_deg 5.65 r_long_range_B_refined 4.498 r_scangle_other 3.954 r_long_range_B_other 3.874 r_rigid_bond_restr 3.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.461 r_sphericity_free 34.795 r_dihedral_angle_4_deg 16.934 r_dihedral_angle_3_deg 12.664 r_sphericity_bonded 12.302 r_dihedral_angle_1_deg 5.65 r_long_range_B_refined 4.498 r_scangle_other 3.954 r_long_range_B_other 3.874 r_rigid_bond_restr 3.456 r_scbond_it 3.289 r_scbond_other 3.288 r_mcangle_other 2.388 r_mcangle_it 2.385 r_mcbond_it 2.056 r_mcbond_other 2.04 r_angle_refined_deg 1.584 r_angle_other_deg 1.009 r_chiral_restr 0.11 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3224 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 21
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement