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Crystal Structure of Cystathionine beta synthase from Legionella pneumophila with LLP, PLP, and homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4COO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 LepnA.01147.a.B1.PW38321 was crystallized at 19.49 mg/ml with 4 mM PLP, 4 mM serine, and 4 mM homocysteine and mixed 1:1 with 0.1 M ammonium acetate, 0.1 M Bis-Tris HCl pH 5.5, and 17% (w/v) PEG 10000. Cryo: 25% EG with 4 mM each ligand. Tray 3295506c1: puck mhb1-1
Crystal Properties Matthews coefficient Solvent content 1.98 37.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.35 α = 90 b = 91.79 β = 90 c = 93.77 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 Beryllium Lenses 2019-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.3 41.22 99.7 0.051 0.056 0.999 15.68 5.269 138423 20.203
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 1.3 1.33 99.9 0.535 0.599 0.893 2.56 4.999
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 THROUGHOUT 4coo 1.3 41.22 1.35 138343 1955 99.65 0.1489 0.1484 0.1483 0.1799 0.1788 20.8074
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4810 Nucleic Acid Atoms Solvent Atoms 598 Heterogen Atoms 111
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing