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Crystal structure of a TRAP periplasmic solute binding protein from Pseudomonas putida F1 (Pput_1203), Target EFI-500184, with bound D-glucuronate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 Protein (60.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-glucuronate); Reservoir (MCSG2(D3), 0.2M Lithium Sulfate, 0.1 M CAPS pH 10.5, 2.0 M Ammonium Sulfate); Cryoprotection (80% Reservoir, 20% glycerol)
Crystal Properties Matthews coefficient Solvent content 1.88 34.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.001 α = 90 b = 35.054 β = 99.54 c = 60.833 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 CCD RAYONIX MX225HE MIRRORS 2014-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 59.99 99.2 0.123 0.06 0.995 9.2 5 53215 10.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.43 99.9 0.78 0.381 0.722 2.3 5 2774
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.4 26.503 1.34 53200 2699 99.07 0.1577 0.1562 0.1573 0.1862 0.1831 12.21
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 13.043 f_angle_d 1.361 f_chiral_restr 0.073 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2377 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 56
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction