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Crystal structure of cystathionine gamma-lyase from Bacillus cereus ATCC 14579
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 2M Ammonium sulfate, 0.1 M Tris-HCl (pH 8.5)
Crystal Properties Matthews coefficient Solvent content 3.06 59.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.708 α = 90 b = 116.708 β = 90 c = 147.794 γ = 90
Symmetry Space Group P 43 21 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 2020-05-12 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) 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 1.98 50 93.7 1 35.02 11.8 71253
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.01 0.505
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 6KHQ 1.98 33.04 63492 3306 93.73 0.2147 0.2122 0.2212 0.2623 0.267 RANDOM 40.012
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] 1.64 1.64 -3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.614 r_dihedral_angle_4_deg 21.883 r_dihedral_angle_3_deg 15.818 r_dihedral_angle_1_deg 7.349 r_angle_refined_deg 1.582 r_angle_other_deg 1.322 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.614 r_dihedral_angle_4_deg 21.883 r_dihedral_angle_3_deg 15.818 r_dihedral_angle_1_deg 7.349 r_angle_refined_deg 1.582 r_angle_other_deg 1.322 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5780 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 81
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing