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Crystal structures of Cystathionine beta lyase from Bacillus cereus ATCC 14579
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7D7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350, Lithium citrate tribasic tetrahydrate
Crystal Properties Matthews coefficient Solvent content 2.75 55.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.1 α = 90 b = 143.1 β = 90 c = 80.907 γ = 120
Symmetry Space Group P 62 2 2
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 ADSC QUANTUM 270 2022-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 2.2 50 99.9 0.069 0.07 0.011 1 14 41.6 25215
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 2.2 2.24 100 0.298 0.302 0.046 0.998 42
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7D7O 2.2 32.74 23904 1235 99.63 0.18343 0.18078 0.1908 0.23291 0.2373 RANDOM 41.448
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] -0.02 -0.01 -0.02 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.294 r_dihedral_angle_4_deg 18.632 r_dihedral_angle_3_deg 16.183 r_long_range_B_refined 7.809 r_long_range_B_other 7.805 r_dihedral_angle_1_deg 6.887 r_scangle_other 6.608 r_mcangle_it 4.778 r_mcangle_other 4.777 r_scbond_other 4.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.294 r_dihedral_angle_4_deg 18.632 r_dihedral_angle_3_deg 16.183 r_long_range_B_refined 7.809 r_long_range_B_other 7.805 r_dihedral_angle_1_deg 6.887 r_scangle_other 6.608 r_mcangle_it 4.778 r_mcangle_other 4.777 r_scbond_other 4.633 r_scbond_it 4.629 r_mcbond_it 3.674 r_mcbond_other 3.665 r_angle_refined_deg 1.607 r_angle_other_deg 1.374 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2937 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction