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Crystal structure of a trap periplasmic solute binding protein from burkholderia ambifaria (Bamb_6123), TARGET EFI-510059, with bound glycerol and chloride ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 298 Protein (16.23 mg/ml, 10 mM HEPES pH 7.5, 150mM NaCl, 5% glycerol, 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% Reservoir, 80% of 50% PEG3350), sitting drop vapor diffusion, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.098 α = 90 b = 97.34 β = 90 c = 58.115 γ = 90
Symmetry Space Group C 2 2 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 CCD RAYONIX MX225HE MIRRORS 2013-07-02 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 2.1 68.386 100 0.136 0.136 11.3 7.2 16289 16289
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 2.1 2.21 100 0.668 0.668 1.2 6.8 2341
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 (All) 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 2PFY 2.1 48.67 16269 16269 820 99.86 0.1574 0.1574 0.1542 0.1585 0.2199 0.2211 RANDOM 25.7937
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 13.637 f_angle_d 1.031 f_chiral_restr 0.07 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2336 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 8
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction BALBES phasing