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Crystal structure of Staphylococcus aureus cystathionine gamma lyase holoenzyme in the presence of NL1F3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IXZ PDB entry 4IXZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 291 0.1 M HEPES sodium, pH 7.6, 1.4 M tri-sodium citrate
Crystal Properties Matthews coefficient Solvent content 4.76 74.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.791 α = 90 b = 104.791 β = 90 c = 287.866 γ = 90
Symmetry Space Group I 41 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 EIGER2 X 16M 2019-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.91956 NSLS-II 17-ID-2
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 2.12 30 99.8 0.247 0.061 0.967 7.9 16.6 45500 33.53
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 2.12 2.16 97.8 0.777 0.23 0.871 0.7 8.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4IXZ 2.12 29.66 1.35 45500 3745 98.72 0.1723 0.1711 0.1695 0.1976 0.197 37.77
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.8097 f_angle_d 0.9052 f_chiral_restr 0.0637 f_bond_d 0.0067 f_plane_restr 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2902 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement autoPROC data processing HKL-2000 data scaling HKL-2000 data reduction PHASER phasing