☰ Navigation Tabs
Crystal structure of Phosphoserine aminotransferase (SerC) from Stenotrophomonas maltophilia K279a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XK1 PDB entry 4xk1 in two domains per MoRDa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Molecular Dimensions Morpheus screen condition A2: 10% (w/V) 8000, 20% (V/V) ethylene glycol: 30mM of each magnesium chloride, calcium chloride: 100mM MES / imidazole pH 6.5: StmaA.00980.a.B1.PW38764 at 25.7mg/ml: tray: 314406a2: cryo: reservoir + 5% 50mM PLP in DMSO: puck mcj9-7
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.35 α = 84.985 b = 71.62 β = 88.816 c = 89.86 γ = 63.369
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+ 2020-05-06 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 1.6 50 97.4 0.055 0.058 0.999 21.99 8.238 183658 23.637
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 1.6 1.64 89.3 0.609 0.665 0.807 2.71 5.776
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4xk1 in two domains per MoRDa 1.6 48.85 1.98 183643 2019 97.4 0.1563 0.156 0.1566 0.1811 0.1828 0 21.19
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 16.2485 f_angle_d 1.0845 f_chiral_restr 0.066 f_bond_d 0.0102 f_plane_restr 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10783 Nucleic Acid Atoms Solvent Atoms 1938 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing Coot model building