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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 6QP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PET3350, Magnesium formate dihydrate
Crystal Properties Matthews coefficient Solvent content 2.08 40.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.67 α = 90 b = 85.233 β = 90 c = 167.965 γ = 90
Symmetry Space Group P 21 21 21
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 2022-04-12 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 1.99 50 95.7 0.079 0.083 0.024 0.996 13.7 11.7 50383
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 2.03 90.5 0.299 0.313 0.088 0.975 11.9
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 6QP3 1.99 33.15 47707 2488 95.41 0.19493 0.19257 0.202 0.23929 0.2432 RANDOM 20.305
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] 0.03 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.981 r_dihedral_angle_4_deg 17.711 r_dihedral_angle_3_deg 14.923 r_long_range_B_other 8.376 r_long_range_B_refined 8.372 r_dihedral_angle_1_deg 7.092 r_scangle_other 3.894 r_scbond_it 2.509 r_scbond_other 2.498 r_mcangle_it 2.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.981 r_dihedral_angle_4_deg 17.711 r_dihedral_angle_3_deg 14.923 r_long_range_B_other 8.376 r_long_range_B_refined 8.372 r_dihedral_angle_1_deg 7.092 r_scangle_other 3.894 r_scbond_it 2.509 r_scbond_other 2.498 r_mcangle_it 2.463 r_mcangle_other 2.463 r_mcbond_it 1.676 r_mcbond_other 1.675 r_angle_refined_deg 1.541 r_angle_other_deg 1.309 r_chiral_restr 0.073 r_bond_refined_d 0.009 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 6004 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing HKL-2000 data reduction