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Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, ligand-free form
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 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.317 α = 90 b = 142.716 β = 114.04 c = 157.008 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 ADSC QUANTUM 270 2014-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 2.36 143.39 98.5 0.066 17.2 3.7 211221
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 2.36 2.4 70 0.291 0.854 2.5 3
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 2.36 143.39 200741 10451 99.42 0.18466 0.1818 0.1891 0.23976 0.2443 RANDOM 39.763
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] -0.01 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.936 r_dihedral_angle_3_deg 14.89 r_dihedral_angle_4_deg 14.68 r_dihedral_angle_1_deg 8.317 r_long_range_B_refined 6.156 r_long_range_B_other 6.131 r_scangle_other 4.27 r_mcangle_it 4.018 r_mcangle_other 4.018 r_scbond_it 2.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.936 r_dihedral_angle_3_deg 14.89 r_dihedral_angle_4_deg 14.68 r_dihedral_angle_1_deg 8.317 r_long_range_B_refined 6.156 r_long_range_B_other 6.131 r_scangle_other 4.27 r_mcangle_it 4.018 r_mcangle_other 4.018 r_scbond_it 2.784 r_scbond_other 2.784 r_mcbond_other 2.71 r_mcbond_it 2.709 r_angle_refined_deg 1.685 r_angle_other_deg 1.037 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_bond_other_d 0.007 r_gen_planes_refined 0.007 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 35774 Nucleic Acid Atoms Solvent Atoms 1098 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing