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The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-biose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 293 22% PEG MME 550, 0.1M 2-Morpholinoethanesulfonic acid monohydrate, 0.01M zinc sulfate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.326 α = 90 b = 143.551 β = 90 c = 114.644 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 210 2006-10-17 M MAD 2 1 100 CCD ADSC QUANTUM 4 2006-11-05
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.970909, 0.97064 Photon Factory BL-17A
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 1.85 50 99 0.047 42.2 7.2 74117 22.4
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 1.85 1.92 98.3 0.264 5.2 6.3 7268
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 (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 1.85 29.75 74117 70377 3726 99.01 0.18767 0.18501 0.1837 0.23785 0.2372 RANDOM 25.494
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 r_dihedral_angle_2_deg 38.986 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 6.225 r_dihedral_angle_4_deg 5.067 r_scangle_it 3.488 r_scbond_it 2.383 r_angle_refined_deg 1.518 r_mcangle_it 1.474 r_mcbond_it 0.935 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.986 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 6.225 r_dihedral_angle_4_deg 5.067 r_scangle_it 3.488 r_scbond_it 2.383 r_angle_refined_deg 1.518 r_mcangle_it 1.474 r_mcbond_it 0.935 r_nbtor_refined 0.306 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.195 r_symmetry_vdw_refined 0.191 r_metal_ion_refined 0.173 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.108 r_symmetry_metal_ion_refined 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6019 Nucleic Acid Atoms Solvent Atoms 948 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing