☰ Navigation Tabs
Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, lacto-N-biose complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293.15 0.1 M ammonium fluoride, 0.1 M MES-NaOH, 20-21% (v/v) PEG3350, 5% MPD
Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.035 α = 90 b = 143.625 β = 90 c = 146.18 γ = 90
Symmetry Space Group P 21 21 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 2015-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.82 102.45 96.3 0.076 23.1 4.7 116978
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.85 96.5 0.736 0.811 2 4.7
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 SAD THROUGHOUT 1.82 102.45 114879 1991 96.27 0.18218 0.18126 0.1935 0.23575 0.242 RANDOM 35.297
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 42.031 r_dihedral_angle_4_deg 13.338 r_dihedral_angle_3_deg 12.801 r_dihedral_angle_1_deg 7.839 r_long_range_B_refined 6.061 r_long_range_B_other 5.877 r_scangle_other 4.708 r_mcangle_other 3.858 r_mcangle_it 3.857 r_scbond_it 3.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.031 r_dihedral_angle_4_deg 13.338 r_dihedral_angle_3_deg 12.801 r_dihedral_angle_1_deg 7.839 r_long_range_B_refined 6.061 r_long_range_B_other 5.877 r_scangle_other 4.708 r_mcangle_other 3.858 r_mcangle_it 3.857 r_scbond_it 3.579 r_scbond_other 3.578 r_mcbond_it 3.241 r_mcbond_other 3.24 r_angle_refined_deg 1.867 r_angle_other_deg 1.079 r_chiral_restr 0.123 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8936 Nucleic Acid Atoms Solvent Atoms 1110 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing