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Crystal structure of a dehydrating condensation domain, AmbE-CmodAA, involved in nonribosomal peptide synthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JGP 2JGP, 6OYF experimental model PDB 6OYF 2JGP, 6OYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 AmbE_Cd crystallized at a concentration of 10mg/ml in conditions containing 100mM bis-Tris propane (pH 6.0), 20% PEG3350 and 0.2M sodium iodide.
Cryoprotection was performed by dipping the crystal in a solution containing 20% MPD (hexylene glycol), 0.2M NaCl, 50mM Tris-Cl (pH7.5), 0.2M sodium iodide, 20% PEG 3350 and 100mM bis-Tris propane (pH 6.0) before being flash frozen in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.71 54.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.94 α = 90 b = 106.87 β = 96.252 c = 108.909 γ = 90
Symmetry Space Group I 1 2 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 PIXEL DECTRIS EIGER X 16M 2018-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.14 76.06 99.2 0.987 16.2 3.3 55789 27.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.2 0.257 0.89 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE 2JGP, 6OYF 2.14 44.7 1.34 55789 2000 99.13 0.1912 0.1896 0.1914 0.2323 0.2327 34.19
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 21.8809 f_angle_d 1.123 f_chiral_restr 0.0581 f_bond_d 0.011 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6348 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHENIX phasing