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Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the PLP-Aminoacrylate Intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JBQ PDB entry 1JBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 30% PEG400, 100 mM calcium acetate, 100 mM Tris, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.64 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.465 α = 90 b = 81.465 β = 90 c = 209.486 γ = 120
Symmetry Space Group P 65 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 315r 2015-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.37 50 99.6 0.104 0.107 0.025 7.1 20.1 86357
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.39 99.5 0.352 0.86 12.6
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 PDB entry 1JBQ 1.37 50 75277 4072 91.55 0.1355 0.134 0.1341 0.1631 0.1632 RANDOM 18.638
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 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.04 r_sphericity_free 26.327 r_dihedral_angle_4_deg 13.473 r_dihedral_angle_3_deg 11.676 r_sphericity_bonded 11.242 r_dihedral_angle_1_deg 6.058 r_rigid_bond_restr 1.909 r_angle_refined_deg 1.585 r_angle_other_deg 0.988 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.04 r_sphericity_free 26.327 r_dihedral_angle_4_deg 13.473 r_dihedral_angle_3_deg 11.676 r_sphericity_bonded 11.242 r_dihedral_angle_1_deg 6.058 r_rigid_bond_restr 1.909 r_angle_refined_deg 1.585 r_angle_other_deg 0.988 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2675 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement PHENIX phasing HKL-2000 data reduction SCALEPACK data scaling PDB_EXTRACT data extraction