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Cystathionine gamma lyase from Thermobifida fusca in an amino crotonate form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SF4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Well solution comprising 20-30% PEG300, 0.1 M HEPES, 0.2 M MgCl2. 2 uL drops were laid with a 1:1 mixture of well solution and 8 mg/mL protein in 0.1 M HEPES buffer pH 7.0. Crystals were grown overnight and were soaked with S-methylmethionine iodide
Crystal Properties Matthews coefficient Solvent content 3.24 62.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.946 α = 90 b = 116.946 β = 90 c = 116.946 γ = 90
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 MX300HE 2021-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.978720 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 40 99 0.02 1 21.2 21.6 84295
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 0.93 0.333 15.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 39.012 84276 4113 98.991 0.138 0.1371 0.1371 0.156 0.1559 22.288
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 r_dihedral_angle_2_deg 27.499 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_3_deg 13.067 r_dihedral_angle_1_deg 6.637 r_lrange_it 5.071 r_lrange_other 4.891 r_scangle_it 2.615 r_scangle_other 2.614 r_angle_refined_deg 1.89 r_scbond_it 1.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.499 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_3_deg 13.067 r_dihedral_angle_1_deg 6.637 r_lrange_it 5.071 r_lrange_other 4.891 r_scangle_it 2.615 r_scangle_other 2.614 r_angle_refined_deg 1.89 r_scbond_it 1.794 r_scbond_other 1.794 r_angle_other_deg 1.609 r_mcangle_it 1.229 r_mcangle_other 1.229 r_mcbond_it 0.895 r_mcbond_other 0.893 r_nbd_refined 0.225 r_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.18 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.163 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.109 r_metal_ion_refined 0.087 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2820 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing