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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-tetraose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 293 24% 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 2.45 49.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.151 α = 90 b = 143.05 β = 90 c = 113.736 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 315 2006-12-14 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 BL-5A 1.0 Photon Factory BL-5A 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 1.65 50 99 0.059 33.1 4 103049 24.4
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 1.65 1.71 97.7 0.369 2.6 3.8 5985
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.65 30.27 97852 5154 98.92 0.18033 0.17859 0.1776 0.21405 0.2127 RANDOM 25.755
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 38.423 r_dihedral_angle_3_deg 12.862 r_dihedral_angle_1_deg 5.673 r_dihedral_angle_4_deg 4.197 r_scangle_it 3.317 r_scbond_it 2.096 r_angle_refined_deg 1.341 r_mcangle_it 1.29 r_mcbond_it 0.72 r_metal_ion_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.423 r_dihedral_angle_3_deg 12.862 r_dihedral_angle_1_deg 5.673 r_dihedral_angle_4_deg 4.197 r_scangle_it 3.317 r_scbond_it 2.096 r_angle_refined_deg 1.341 r_mcangle_it 1.29 r_mcbond_it 0.72 r_metal_ion_refined 0.326 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.246 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.16 r_symmetry_metal_ion_refined 0.147 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 972 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing