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Crystal Structure of an ABC transporter periplasmic solute binding protein (IPR025997) from Actinobacillus succinogenes 130z(Asuc_0081, TARGET EFI-511065) with bound D-allose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 Protein (10 mM D-allose, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (1.0 M Lithium chloride, 0.1 M sodium citrate:HCl pH 4.0, 20% (w/v) PEG 6000); Cryoprotection (20% Ethylene glycol, 80% Reservoir)
Crystal Properties Matthews coefficient Solvent content 1.98 37.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.19 α = 101.13 b = 63.218 β = 103.29 c = 71.201 γ = 91.35
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 2015-08-15 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) Rrim I (All) 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 2.29 42 63.1 0.114 0.133 0.072 7.5 3.4 28967 30.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.33 9.2 0.821 0.445 2.4 206
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2IOY 2.7 33.147 1.97 24765 1180 87.31 0.1698 0.1644 0.1702 0.2752 0.2726 28.6742
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 16.002 f_angle_d 1.196 f_chiral_restr 0.045 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8631 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 48
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction BALBES phasing