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The structure of a family 1 extracellular solute-binding protein from Bifidobacterium longum subsp. infantis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 294 0.1M sodium acetate pH 4.6, 2.5M ammonium sulfate, 1/10 papain, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.02 38.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.532 α = 90 b = 105.095 β = 90 c = 145.375 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 CCD ADSC QUANTUM 315r 2010-07-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97935, 0.97921 APS 19-ID
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 1.6 50 98.1 0.081 9 4.6 95082 95082 -3 20.1
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) 1.6 1.63 95 0.582 4.2 4569
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.7 48.27 79400 79400 3974 98.15 0.1523 0.1523 0.1509 0.1648 0.1804 0.1915 RANDOM 24.077
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] 1.42 -0.55 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.17 r_dihedral_angle_4_deg 19.918 r_dihedral_angle_3_deg 13.703 r_dihedral_angle_1_deg 5.244 r_scangle_it 4.748 r_scbond_it 2.879 r_mcangle_it 1.743 r_angle_refined_deg 1.417 r_mcbond_it 0.945 r_angle_other_deg 0.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.17 r_dihedral_angle_4_deg 19.918 r_dihedral_angle_3_deg 13.703 r_dihedral_angle_1_deg 5.244 r_scangle_it 4.748 r_scbond_it 2.879 r_mcangle_it 1.743 r_angle_refined_deg 1.417 r_mcbond_it 0.945 r_angle_other_deg 0.895 r_mcbond_other 0.267 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5996 Nucleic Acid Atoms Solvent Atoms 825 Heterogen Atoms 33
Software Software Software Name Purpose SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building