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Crystal structure of E. coli phosphatidylserine synthase complexed with 16:0/16:0 CDP-DG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P23830-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 0.1 M Lithium sulfate monohydrate, 0.1 M ADA pH 6.5, 12% polyethylene glycol, 2 % (w/v) 2-propanol, 0.5 %(w/v) DDM
Crystal Properties Matthews coefficient Solvent content 3.19 61.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.497 α = 90 b = 160.497 β = 90 c = 160.497 γ = 90
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 EIGER X 9M 2022-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.000 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.44 42.89 100 0.256 0.26 0.041 0.998 11 40.5 25695
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.54 100 5.209 5.276 0.836 0.483 39.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.44 42.89 24360 1268 99.83 0.21406 0.21233 0.2229 0.24698 0.2557 RANDOM 65.996
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 r_dihedral_angle_3_deg 11.892 r_dihedral_angle_1_deg 6.7 r_dihedral_angle_2_deg 4.935 r_long_range_B_other 4.761 r_long_range_B_refined 4.76 r_scangle_other 2.986 r_mcangle_it 2.794 r_mcangle_other 2.794 r_scbond_it 1.712 r_scbond_other 1.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.892 r_dihedral_angle_1_deg 6.7 r_dihedral_angle_2_deg 4.935 r_long_range_B_other 4.761 r_long_range_B_refined 4.76 r_scangle_other 2.986 r_mcangle_it 2.794 r_mcangle_other 2.794 r_scbond_it 1.712 r_scbond_other 1.709 r_mcbond_it 1.682 r_mcbond_other 1.682 r_angle_refined_deg 1.067 r_angle_other_deg 0.456 r_chiral_restr 0.048 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3660 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement MxDC data collection xia2 data reduction DIALS data reduction Aimless data scaling MOLREP phasing Coot model building PDB_EXTRACT data extraction