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Cystathionine gamma lyase from Thermobifida fusca in internal aldimine form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X5H
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
Crystal Properties Matthews coefficient Solvent content 3.24 62.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.591 α = 90 b = 117.591 β = 90 c = 117.591 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) 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 1.455 40.003 100 0.075 1 25.36 22.1 94728
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.49 100 1.697 0.748 2.09 21.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.455 40.003 94728 4687 99.964 0.134 0.133 0.1481 0.1525 20.789
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 29.09 r_dihedral_angle_4_deg 20.121 r_dihedral_angle_3_deg 11.996 r_dihedral_angle_1_deg 6.581 r_lrange_it 5.077 r_lrange_other 4.916 r_scangle_other 2.842 r_scangle_it 2.832 r_angle_refined_deg 2.248 r_scbond_it 1.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.09 r_dihedral_angle_4_deg 20.121 r_dihedral_angle_3_deg 11.996 r_dihedral_angle_1_deg 6.581 r_lrange_it 5.077 r_lrange_other 4.916 r_scangle_other 2.842 r_scangle_it 2.832 r_angle_refined_deg 2.248 r_scbond_it 1.994 r_scbond_other 1.959 r_angle_other_deg 1.679 r_mcangle_other 1.325 r_mcangle_it 1.324 r_mcbond_it 0.96 r_mcbond_other 0.943 r_symmetry_xyhbond_nbd_other 0.282 r_symmetry_xyhbond_nbd_refined 0.231 r_nbd_refined 0.227 r_xyhbond_nbd_other 0.223 r_nbtor_refined 0.173 r_nbd_other 0.173 r_symmetry_nbd_other 0.172 r_symmetry_nbd_refined 0.164 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.118 r_symmetry_nbtor_other 0.089 r_metal_ion_refined 0.038 r_bond_refined_d 0.02 r_gen_planes_refined 0.015 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2835 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing