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Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with 8-bromooctanoic acid
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 5.5 289 1.5 UL PROTEIN + 1.5 UL BUFFER (35% PEG3350, 0.1 M SODIUM CACODYLATE, 0.2 M SODIUM CHLORIDE, PH 5.75)
Crystal Properties Matthews coefficient Solvent content 2.04 39.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.968 α = 90 b = 67.757 β = 115.73 c = 54.193 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 1.55 50 99.9 0.044 14.4 4.2 47386
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 1.55 1.58 100 0.398 4.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5IBY 1.55 48 44806 2392 99.81 0.1802 0.1782 0.2167 0.2328 RANDOM 24.408
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] 0.39 0.19 0.49 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.467 r_dihedral_angle_4_deg 15.02 r_dihedral_angle_3_deg 11.504 r_dihedral_angle_1_deg 6.279 r_mcangle_it 2.789 r_mcbond_it 2.187 r_mcbond_other 2.181 r_angle_refined_deg 1.204 r_angle_other_deg 0.722 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.467 r_dihedral_angle_4_deg 15.02 r_dihedral_angle_3_deg 11.504 r_dihedral_angle_1_deg 6.279 r_mcangle_it 2.789 r_mcbond_it 2.187 r_mcbond_other 2.181 r_angle_refined_deg 1.204 r_angle_other_deg 0.722 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2556 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction DENZO data reduction