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Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with 8BO-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 (27% PEG3350, 0.1 M SODIUM CACODYLATE, 0.2 M SODIUM CHLORIDE, PH 5.25)
Crystal Properties Matthews coefficient Solvent content 2.13 42.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.917 α = 90 b = 69.383 β = 92.3 c = 97.664 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 ADSC QUANTUM 210r 2014-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97905 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.85 50 99.8 0.037 0.041 0.018 23.7 4.9 58160
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 100 0.126 0.145 0.07 0.984 4.1 5822
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 1.85 21.5 55147 2935 99.79 0.1712 0.1694 0.1794 0.2052 0.2129 RANDOM 23.297
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 0.03 1.1 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.719 r_dihedral_angle_4_deg 16.051 r_dihedral_angle_3_deg 12.019 r_dihedral_angle_1_deg 6.057 r_mcangle_it 1.662 r_angle_refined_deg 1.186 r_mcbond_it 1.029 r_mcbond_other 1.029 r_angle_other_deg 0.722 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.719 r_dihedral_angle_4_deg 16.051 r_dihedral_angle_3_deg 12.019 r_dihedral_angle_1_deg 6.057 r_mcangle_it 1.662 r_angle_refined_deg 1.186 r_mcbond_it 1.029 r_mcbond_other 1.029 r_angle_other_deg 0.722 r_chiral_restr 0.075 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 5124 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction DENZO data reduction