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Crystal Structure of Phosphoserine aminotransferase from Klebsiella pneumoniae subsp. pneumoniae in complex with Pyridoxal phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.7 287 Optimization condition around Anatrace/Calibre MCSG1 screen D9: 100mM Tris Base/HCl pH 8.7, 28% PEG 3350, 200mM NaCl: KlpnC.00980.a.B1.PW39015 at 27mg/ml + 3.5mM PLP: tray 323619 g9: cryo: 20% EG+ 2.5mM PLP in 2 steps, puck: bid6-5.
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.21 α = 90 b = 80.66 β = 104.065 c = 86.82 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 CCD RIGAKU SATURN 944+ Beryllium Lenses 2021-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.5 50 99.6 0.032 0.033 1 53.85 16.407 117524 21.155
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 96.4 0.443 0.47 0.924 4.66 8.359
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD FREE R-VALUE 1.5 44.62 1.35 117496 2021 99.61 0.129 0.1284 0.1286 0.1602 0.1608 0 18.63
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.5806 f_angle_d 0.9361 f_chiral_restr 0.0567 f_bond_d 0.0085 f_plane_restr 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5522 Nucleic Acid Atoms Solvent Atoms 1003 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction SHELXDE phasing Coot model building SHELXE model building