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Crystal structure of LplA1 in complex with lipoic acid (Listeria monocytogenes)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 200 mM NH4Cl, 2.2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.57 52.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.87 α = 90 b = 72.79 β = 98.04 c = 93.05 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 2.1 30 97.1 0.055 10.7 2.9 44270
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 2.1 2.2 98.9 0.66 2.1 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 2.1 30 42047 2213 97.11 0.22487 0.22334 0.2246 0.25145 0.2572 RANDOM 47.39
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] 2.66 -6.14 -1.41 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.072 r_dihedral_angle_4_deg 14.634 r_dihedral_angle_3_deg 13.765 r_dihedral_angle_1_deg 6.483 r_long_range_B_refined 2.618 r_long_range_B_other 2.561 r_mcangle_it 1.648 r_mcangle_other 1.647 r_scangle_other 1.348 r_angle_refined_deg 1.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.072 r_dihedral_angle_4_deg 14.634 r_dihedral_angle_3_deg 13.765 r_dihedral_angle_1_deg 6.483 r_long_range_B_refined 2.618 r_long_range_B_other 2.561 r_mcangle_it 1.648 r_mcangle_other 1.647 r_scangle_other 1.348 r_angle_refined_deg 1.155 r_mcbond_it 1.15 r_mcbond_other 1.15 r_angle_other_deg 1.046 r_scbond_it 0.943 r_scbond_other 0.943 r_rigid_bond_restr 0.514 r_chiral_restr 0.036 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_refined 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 4710 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing