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CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER sp. NAS-14.1 (TARGET EFI-510299) WITH BOUND BETA-D-GALACTURONATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 Protein (31.8 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Galacturonate); Reservoir (2.4 M Sodium Malonate pH 7.0); Cryoprotection (80% Reservoir + 20% Diethylene Glycol
Crystal Properties Matthews coefficient Solvent content 2.46 49.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.979 α = 115.62 b = 58.014 β = 104.69 c = 62.968 γ = 94.16
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 2014-04-02 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) Rpim I (All) 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 53.85 94.8 0.095 0.056 10.9 3.9 106185 14.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 93.6 0.698 0.406 2.3 4 5175
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4OVQ 1.5 27.923 1.96 106184 10400 92.73 0.1482 0.1473 0.1578 0.165 0.1736 Random Selection 18.16
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 12.929 f_angle_d 1.299 f_chiral_restr 0.074 f_bond_d 0.011 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4586 Nucleic Acid Atoms Solvent Atoms 766 Heterogen Atoms 28
Software Software Software Name Purpose PDB_EXTRACT data extraction PHENIX refinement Aimless data scaling