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Crystal structure of holo-ObiF1, a five domain nonribosomal peptide synthetase from Burkholderia diffusa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U89 5U89, 5T3D, 3FLB experimental model PDB 5T3D 5U89, 5T3D, 3FLB experimental model PDB 3FLB 5U89, 5T3D, 3FLB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.8 287 well solution: 90 mM HEPES pH 6.8, 5% w/v 1,3-dimethylimidazolium dimethyl phosphate, 27% w/v PEG3350; protein sample: 25 mM HEPES pH 8.0, 25 mM NaCl, 0.4 mM TCEP, 5% v/v glycerol, 36.5 mg/mL holo-ObiF1; drop composition: 2 uL protein: 1 uL well solution under paraffin oil
Crystal Properties Matthews coefficient Solvent content 3.79 67.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.325 α = 90 b = 154.345 β = 90 c = 183.905 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2018-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3 39.7034 99.9 0.096 0.105 0.041 0.995 11.4 6.4 47131 64.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 99.9 0.407 0.442 0.171 0.938 3.3 6.6
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 5U89, 5T3D, 3FLB 3 39.703 1.98 47061 1998 99.84 0.2116 0.2103 0.2136 0.24 0.2447 79.0011
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 9937 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 93
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling PHASER phasing