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Structure of a thiolation-reductase di-domain from an archaeal non-ribosomal peptide synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 293.15 Crystals were grown by vapor diffusion, sitting drop method. Drop volume was 2 micro-liter (1+1) equilibrated against 50 micro-liter of reservoir volume of 1.7 M malic acid at pH 6.1. The concentration of protein was 30 mg/ml in HEPES buffer at pH 7.5 containing 150 mM of NaCl
Crystal Properties Matthews coefficient Solvent content 2.61 52.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.949 α = 90 b = 71.833 β = 90.26 c = 82.725 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 EIGER X 16M 2018-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.948 47.636 92.4 0.993 5.48 3.82 40262 32.22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.07 0.126
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 4F6C 1.95 47.62 1.33 39055 1927 91.9 0.198 0.196 0.202 0.239 0.2431 37.17
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 3715 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing