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Crystal Structure of the N-prenyltransferase DabA in Complex with GSPP and Mg2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 282 1.5 M sodium citrate
0.05 M HEPES pH 7.5
4 mg/mL DabA preincubated with 2 mM GSPP, 5 mM MgCl2, and 50 mM L-Glu
Crystal Properties Matthews coefficient Solvent content 4.29 71.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.286 α = 90 b = 124.286 β = 90 c = 114.483 γ = 90
Symmetry Space Group P 43 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 CCD ADSC QUANTUM 315r 2019-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 42.102 94.9 0.13 0.039 0.999 16.6 11.8 50088 27.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.107 100 1.194 0.359 0.776 3.2 12.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.1 42.1 1.34 50064 2560 94.82 0.1674 0.1662 0.1672 0.1877 0.1884 33.72
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.0647 f_angle_d 0.7714 f_chiral_restr 0.0452 f_bond_d 0.0065 f_plane_restr 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3530 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction autoPROC data scaling AutoSol phasing