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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-galacturonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LNM PDB ENTRY 4LNM
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-galacturonic acid, reservoir: 0.2 M calcium acetate, 0.1 M MES, pH 6.0, 20% w/v PEG8000 (MCSG1 B6), cryoprotection: 4:1 50% w/v PEG3350:reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.84 33.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.152 α = 90 b = 101.369 β = 90 c = 55.72 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 2013-09-17 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 1.5 100 99.4 0.07 0.07 12 8 43587 43587 14.35
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 1.5 1.53 91.8 0.588 4.4 1974
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 4LNM 1.501 24.415 42548 42548 2137 97 0.1719 0.1719 0.1703 0.1706 0.2015 0.2008 RANDOM 20.6846
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 13.176 f_angle_d 1.338 f_chiral_restr 0.071 f_bond_d 0.015 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2317 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 16
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction StructureStudio data collection HKL-3000 data reduction HKL-3000 phasing