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Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, locus tag GOS_1523157, Triple Surface Mutant K158A_K223A_K313A) in complex with metahydroxyphenylacetate, thermal exchange of ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I7I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM 3-Hydroxyphenylacetic acid, soak 30 minutes at 60 C); Reservoir (MCSG1 (A2), 0.1 M CHES pH 9.5, 30 %(w/v) PEG 3000); Cryoprotection (20% diethylene glycol, 80% reservoir)
Crystal Properties Matthews coefficient Solvent content 1.92 35.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.784 α = 90 b = 84.275 β = 113.48 c = 45.91 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 200K mirrors 2016-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54056
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 100 94 0.052 0.059 0.027 12.3 4.1 34550 8.81
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 1.6 1.63 80.3 0.265 0.322 0.18 0.866 2.8 1470
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 5I7I 1.6 29.786 1.37 34431 1724 94.04 0.1166 0.1147 0.1163 0.1531 0.1545 13.2012
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 15.395 f_angle_d 0.99 f_chiral_restr 0.056 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2398 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 103
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction MOLREP phasing HKL-3000 data reduction