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Crystal structure of PksD, the trans-acting acyl hydrolase domain from the bacillaene trans-AT PKS (native)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMet-derived PksD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 0.1 M Tris pH 8.5, 10% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.76 67.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.202 α = 90 b = 163.33 β = 104.5 c = 186.871 γ = 90
Symmetry Space Group C 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 EIGER2 XE 16M 2019-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976280 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.2 90.46 99.5 0.064 0.069 0.026 0.999 15.2 6.9 220807
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 2.2 2.24 91.6 2.815 3.166 1.411 0.223 4.7
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 THROUGHOUT SeMet-derived PksD 2.2 51.08 1.34 220207 11227 99.23 0.1993 0.1978 0.2014 0.2273 0.2293 75.4819
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20149 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 4
Software Software Software Name Purpose PDB_EXTRACT data extraction PHENIX refinement PHASER phasing Aimless data scaling XDS data reduction