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The crystal structure of acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II-like protein from Dyadobacter fermentans DSM 18053
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.2M Ammonium Iodine,
20% (w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.148 α = 90 b = 67.148 β = 90 c = 176.257 γ = 90
Symmetry Space Group P 43 2 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 315 mirror 2012-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID
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 2.018 33 99.6 0.085 31.2 7.1 27429 27429
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 2.02 2.05 99.9 0.602 3.6 7.2 1340
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD 2.018 32.981 1.34 27373 27373 1373 99.68 0.1984 0.1984 0.1956 0.1886 0.2545 0.2449 Random
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] 3.3829 3.3829 -6.7658
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.012 f_angle_d 1.015 f_chiral_restr 0.069 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2681 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 60
Software Software Software Name Purpose SBC-Collect data collection SHELXD phasing MLPHARE phasing DM model building RESOLVE model building HKL-3000 phasing PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing