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Crystal structure of a TRAP periplasmic solute binding protein from Burkholderia ambifaria (BAM_6123), Target EFI-510059, with bound beta-D-glucuronate
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 7.5 298 59.1 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-glucuronic acid, reservoir: 0.2 M magnesium acetate, 20% w/v PEG3350 (MCSG1 C5), cryoprotection: 4:1 50% w/v PEG3350:reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.84 33.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.19 α = 90 b = 101.781 β = 90 c = 55.522 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2013-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
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 1.65 100 97.6 0.064 0.064 14.5 4.6 32282 32282 14.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 90 0.365 3.1 1473
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 PDB ENTRY 4LN5 1.651 22.067 31126 31126 1572 94.03 0.1603 0.1603 0.1583 0.161 0.1955 0.1958 RANDOM 22.7023
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 13.004 f_angle_d 1.273 f_chiral_restr 0.074 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2327 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction StructureStudio data collection HKL-3000 data reduction AMoRE phasing