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Crystal structure of Cystathionine beta-lyase from Klebsiella pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FQ6 PDB entry 2FQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 287 1:1 27 mg/mL KlpnC.00906.a.B1.PW38994 to JCSG_TOP96(a5) (40% v/v MPD, 100 mM HEPES free acid/ NaOH, pH 6.5), harvested and frozen directly, puck: yis2-8, barcode: 321997a5
Crystal Properties Matthews coefficient Solvent content 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.61 α = 90 b = 131.14 β = 99.93 c = 85.44 γ = 90
Symmetry Space Group P 1 21 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 CCD RAYONIX MX-300 Beryllium Lenses 2021-07-29 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 1.9 45.91 99.9 0.126 0.135 0.997 14.94 7.502 140666 15.37
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 1.9 1.95 99.9 0.591 0.634 0.9 4.81 7.596
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 2FQ6 1.9 45.91 1.36 140628 2090 99.95 0.1637 0.1632 0.1633 0.1954 0.1956 17.7046
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 12066 Nucleic Acid Atoms Solvent Atoms 1701 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XDS data reduction PDB_EXTRACT data extraction XSCALE data scaling MoRDa phasing