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Crystal structure of a Trap periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_3107), target EFI-510173, with bound alpha/beta D-Galacturonate, space group P21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LN5 PDB entry 4LN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein (50 mg/ml, 10 mM Hepes, pH 7.5, 10 mM Galacturonate, 5 mM DTT); Reservoir (0.8 M Lithium Chloride, 0.1 M Tris, pH 8.5, 32 %(w/v) PEG 4000, (MCSG1 C9)); Cryoprotection (20% Ethylene Glycol, 80% of Reservoir), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.82 32.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.534 α = 90 b = 46.14 β = 97.56 c = 63.897 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 CCD RAYONIX MX225HE MIRRORS 2013-07-23 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) R Sym I (Observed) 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 1.1 63.341 97.6 0.061 0.061 9.6 3.6 104054 104054 7.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 84 0.299 0.299 2.2 2.8 13016
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 4LN5 1.1 34.665 104014 104014 5187 97.62 0.1387 0.138 0.1376 0.1516 0.1515 RANDOM 13.8665
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 12.126 f_angle_d 1.287 f_chiral_restr 0.077 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2319 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 33
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction AMoRE phasing