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Closed liganded crystal structure of xylose binding protein from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IOY PDB entry 2IOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 296 2.4M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.56 65.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.064 α = 90 b = 156.064 β = 90 c = 103.609 γ = 120
Symmetry Space Group P 32 2 1
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 ADSC QUANTUM 315r 2008-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9762 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 20 0.099 141545
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 2.2 2.32 0.4 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB entry 2IOY 2.2 20 134285 7075 98.79 0.18306 0.18208 0.1793 0.20163 0.1971 RANDOM 27.429
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] 0.36 0.18 0.36 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.429 r_dihedral_angle_4_deg 15.902 r_dihedral_angle_3_deg 14.602 r_dihedral_angle_1_deg 5.472 r_scangle_it 4.115 r_scbond_it 2.365 r_angle_refined_deg 1.314 r_mcangle_it 1.288 r_mcbond_it 0.643 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.429 r_dihedral_angle_4_deg 15.902 r_dihedral_angle_3_deg 14.602 r_dihedral_angle_1_deg 5.472 r_scangle_it 4.115 r_scbond_it 2.365 r_angle_refined_deg 1.314 r_mcangle_it 1.288 r_mcbond_it 0.643 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7050 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 30
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling