☰ Navigation Tabs
Crystal structure of lacto-N-biosidase BsaX from Bifidobacterium saguini, lacto-N-biose complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 0.5M ammonium sulfate, 0.1M sodium acetate (pH 4.6), 30% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.24 45.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.24 α = 90 b = 113.24 β = 90 c = 79.097 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS PILATUS3 S 6M 2018-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.51 49.08 100 0.184 0.194 0.061 0.995 11.2 10 20374 15.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.51 2.61 100 0.695 0.732 0.228 0.913 3.8 10.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 5GQF 2.51 49.08 19380 972 99.98 0.15995 0.15664 0.1658 0.22759 0.2316 RANDOM 25.598
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] 0.65 0.33 0.65 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.892 r_dihedral_angle_4_deg 22.526 r_dihedral_angle_3_deg 14.287 r_dihedral_angle_1_deg 8.872 r_long_range_B_other 4.821 r_long_range_B_refined 4.819 r_scangle_other 3.502 r_mcangle_it 2.686 r_mcangle_other 2.686 r_scbond_it 2.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.892 r_dihedral_angle_4_deg 22.526 r_dihedral_angle_3_deg 14.287 r_dihedral_angle_1_deg 8.872 r_long_range_B_other 4.821 r_long_range_B_refined 4.819 r_scangle_other 3.502 r_mcangle_it 2.686 r_mcangle_other 2.686 r_scbond_it 2.235 r_scbond_other 2.228 r_mcbond_it 1.786 r_mcbond_other 1.785 r_angle_refined_deg 1.655 r_angle_other_deg 1.305 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 4617 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing