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Crystal structure of E. coli phosphatidylserine synthase in apo state
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, SITTING DROP 5.9 297 0.09 M Sodium citrate tribasic dihydrate pH 5.9, 0.09 M Lithium sulfate monohydrate, 0.1 M Sodium malonate pH 7.0, 12.6 % (w/v) polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.04 α = 88.24 b = 94.1 β = 87.7 c = 194.75 γ = 60.07
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 2021-07-28 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 2.83 48.64 98.2 0.187 0.207 0.088 0.995 8.1 5.3 135369
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 2.83 2.88 98 1.86 2.063 0.882 0.36 5.3
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 2.83 48.64 129010 6358 98.16 0.24394 0.2419 0.2416 0.28478 0.2795 RANDOM 71.2
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] -2.13 3.5 -2.14 1.94 -1.01 2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.865 r_long_range_B_refined 12.763 r_long_range_B_other 12.763 r_scangle_other 9.257 r_mcangle_it 9.243 r_mcangle_other 9.243 r_dihedral_angle_2_deg 7.063 r_dihedral_angle_1_deg 6.844 r_mcbond_it 5.864 r_mcbond_other 5.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.865 r_long_range_B_refined 12.763 r_long_range_B_other 12.763 r_scangle_other 9.257 r_mcangle_it 9.243 r_mcangle_other 9.243 r_dihedral_angle_2_deg 7.063 r_dihedral_angle_1_deg 6.844 r_mcbond_it 5.864 r_mcbond_other 5.864 r_scbond_it 5.682 r_scbond_other 5.658 r_angle_refined_deg 1.329 r_angle_other_deg 0.477 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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 43775 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 120
Software Software Software Name Purpose MxDC data collection autoPROC data processing XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction