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Crystal structure of LplA1 in complex with lipoyl-AMP (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 6 293 0.1 M MES, 1.0 M LiCl, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 4.61 73.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.31 α = 90 b = 79.31 β = 90 c = 225.14 γ = 90
Symmetry Space Group P 41 21 2
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 2022-08-24 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 98.4 0.053 15.4 4.5 22722
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 0.691 2.4 4.8
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 21558 1135 98.6 0.1747 0.173 0.187 0.2061 0.2144 RANDOM 74.053
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] -0.79 -0.79 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.226 r_dihedral_angle_4_deg 14.685 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_1_deg 6.486 r_angle_refined_deg 1.166 r_angle_other_deg 1.042 r_rigid_bond_restr 0.529 r_chiral_restr 0.04 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.226 r_dihedral_angle_4_deg 14.685 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_1_deg 6.486 r_angle_refined_deg 1.166 r_angle_other_deg 1.042 r_rigid_bond_restr 0.529 r_chiral_restr 0.04 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2710 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing