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Cystathionine beta-lyase from Klebsiella pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 303 50 mM TRIS-HCl, pH 8.5, 55% PEG MME 2000, 0.2 mM PLP, 25 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.418 α = 90 b = 131.209 β = 100.46 c = 84.574 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 PIXEL RIGAKU HyPix-6000HE 2025-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.9 22.89 98.3 0.1 0.109 0.041 0.998 17.2 6.7 136224
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 96.4 0.373 0.405 0.155 0.941 6.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 22.89 129090 6902 97.96 0.16822 0.16629 0.1663 0.20458 0.2046 RANDOM 15.061
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] -1.08 0.69 -0.57 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.716 r_dihedral_angle_2_deg 9.751 r_dihedral_angle_1_deg 6.677 r_long_range_B_refined 4.959 r_scbond_it 2.632 r_mcangle_it 1.988 r_angle_refined_deg 1.962 r_mcbond_it 1.462 r_chiral_restr 0.129 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.716 r_dihedral_angle_2_deg 9.751 r_dihedral_angle_1_deg 6.677 r_long_range_B_refined 4.959 r_scbond_it 2.632 r_mcangle_it 1.988 r_angle_refined_deg 1.962 r_mcbond_it 1.462 r_chiral_restr 0.129 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12037 Nucleic Acid Atoms Solvent Atoms 1533 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction CrysalisPro data reduction MOLREP phasing