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Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with lipoyl-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.25 289 1.5 UL PROTEIN + 1.5 UL BUFFER (31% PEG3350, 0.1 M SODIUM CACODYLATE, 0.2 M SODIUM CHLORIDE, PH 5.25)
Crystal Properties Matthews coefficient Solvent content 2.13 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.942 α = 90 b = 69.35 β = 92.15 c = 97.685 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 CCD MARMOSAIC 300 mm CCD 2013-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 1.8 50 99.7 0.058 11.5 4.2 62746
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 1.8 1.83 99.7 0.354 4.2
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 5IBY 1.8 48 59481 3180 99.33 0.1994 0.1975 0.2038 0.2351 0.2397 RANDOM 28.509
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] -0.36 0.44 1.27 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.507 r_dihedral_angle_4_deg 13.705 r_dihedral_angle_3_deg 11.744 r_dihedral_angle_1_deg 5.99 r_mcangle_it 2.567 r_mcbond_it 1.905 r_mcbond_other 1.905 r_angle_refined_deg 1.165 r_angle_other_deg 0.721 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.507 r_dihedral_angle_4_deg 13.705 r_dihedral_angle_3_deg 11.744 r_dihedral_angle_1_deg 5.99 r_mcangle_it 2.567 r_mcbond_it 1.905 r_mcbond_other 1.905 r_angle_refined_deg 1.165 r_angle_other_deg 0.721 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5183 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction MOLREP phasing DENZO data reduction