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The structure of the periplasmic L-arabinose binding protein from Burkholderia thailandensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ABP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 50% MPD, 200mM Ammonium Phosphate, 100mM Tris pH8.5, 14.8mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.88 34.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.77 α = 90 b = 51.82 β = 107.34 c = 59.22 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD 2013-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97857 APS 21-ID-F
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 1.5 43.73 100 0.111 21.42 11596 -3 20.707
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 1.95 2 100 0.437 6.75
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5ABP 1.5 43.73 2142 99.66 0.1708 0.1696 0.1708 0.1925 0.1948 RANDOM 17.7108
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] -0.15 -0.84 -0.25 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.811 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 11.448 r_dihedral_angle_1_deg 5.305 r_angle_refined_deg 1.272 r_mcangle_it 0.772 r_angle_other_deg 0.766 r_mcbond_it 0.458 r_mcbond_other 0.446 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.811 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 11.448 r_dihedral_angle_1_deg 5.305 r_angle_refined_deg 1.272 r_mcangle_it 0.772 r_angle_other_deg 0.766 r_mcbond_it 0.458 r_mcbond_other 0.446 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2235 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 12
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction