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Crystal structure of LplA1 in complex with the inhibitor C3 (Listeria monocytogenes)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 8CRI Crystal structure of LplA1 in complex with lipoic acid (Listeria monocytogenes)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M TRIS, 0.2 M CaCl2, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.63 53.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.32 α = 90 b = 74.27 β = 98.06 c = 92.73 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 PIXEL DECTRIS EIGER X 16M 2022-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.6 30 96.4 0.08 9.1 3 23850
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 2.6 2.7 98.8 0.673 2.4 3.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8CRI 2.6 30 22646 1192 96.32 0.23687 0.23497 0.2414 0.27321 0.2858 RANDOM 57.491
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] 5.5 -9.11 -2.72 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.186 r_dihedral_angle_3_deg 18.57 r_dihedral_angle_4_deg 15.323 r_dihedral_angle_1_deg 5.862 r_mcangle_it 2.23 r_mcangle_other 2.23 r_scangle_other 2.069 r_mcbond_it 1.563 r_mcbond_other 1.561 r_scbond_it 1.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.186 r_dihedral_angle_3_deg 18.57 r_dihedral_angle_4_deg 15.323 r_dihedral_angle_1_deg 5.862 r_mcangle_it 2.23 r_mcangle_other 2.23 r_scangle_other 2.069 r_mcbond_it 1.563 r_mcbond_other 1.561 r_scbond_it 1.426 r_scbond_other 1.426 r_angle_refined_deg 1.291 r_angle_other_deg 1.232 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4604 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing