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Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with PLP internal aldimine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 0.2 M lithium sulfate, 17% PEG 3350 and 0.1 M Tris at pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.221 α = 90 b = 105.929 β = 90 c = 186.886 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 PIXEL DECTRIS PILATUS 6M 2018-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.57 76.78 99.2 0.089 13.33 7.4 230909 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.66 98.1 0.965 1.85 7.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4XK1 1.57 76.78 229752 1155 99.26 0.15755 0.15745 0.17524 0.1833 RANDOM 21.943
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] 1.24 -0.31 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.193 r_dihedral_angle_4_deg 15.903 r_dihedral_angle_3_deg 12.626 r_dihedral_angle_1_deg 6.366 r_long_range_B_refined 4.992 r_long_range_B_other 4.992 r_scangle_other 2.391 r_angle_refined_deg 1.541 r_scbond_it 1.493 r_scbond_other 1.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.193 r_dihedral_angle_4_deg 15.903 r_dihedral_angle_3_deg 12.626 r_dihedral_angle_1_deg 6.366 r_long_range_B_refined 4.992 r_long_range_B_other 4.992 r_scangle_other 2.391 r_angle_refined_deg 1.541 r_scbond_it 1.493 r_scbond_other 1.493 r_mcangle_other 1.457 r_mcangle_it 1.456 r_mcbond_it 0.907 r_mcbond_other 0.906 r_angle_other_deg 0.844 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 11346 Nucleic Acid Atoms Solvent Atoms 1875 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing