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Crystal structure of lacto-N-biosidase StrLNBase from Streptomyces sp. strain 142, galacto-N-biose complex 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HVB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.25 M Ammonium fluoride, 12.5%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.13 42.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.779 α = 90 b = 60.825 β = 98.19 c = 88.232 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 PIXEL DECTRIS PILATUS3 S 2M 2022-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000000 Photon Factory AR-NW12A
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 1.41 47.99 99.9 0.051 0.061 0.033 0.995 12.4 3.4 107633 10.69
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 1.41 1.43 100 0.482 0.583 0.324 0.784 2.1 3.1
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 MOLECULAR REPLACEMENT THROUGHOUT 1.41 47.94 102255 5355 99.9 0.16594 0.16455 0.1654 0.19273 0.1941 RANDOM 14.688
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] -0.5 0.06 1.3 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.135 r_dihedral_angle_2_deg 7.951 r_dihedral_angle_1_deg 7.245 r_long_range_B_refined 4.683 r_long_range_B_other 4.683 r_scangle_other 3.337 r_mcangle_it 2.249 r_mcangle_other 2.248 r_scbond_it 2.232 r_scbond_other 2.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.135 r_dihedral_angle_2_deg 7.951 r_dihedral_angle_1_deg 7.245 r_long_range_B_refined 4.683 r_long_range_B_other 4.683 r_scangle_other 3.337 r_mcangle_it 2.249 r_mcangle_other 2.248 r_scbond_it 2.232 r_scbond_other 2.231 r_angle_refined_deg 1.724 r_mcbond_it 1.572 r_mcbond_other 1.565 r_angle_other_deg 0.572 r_chiral_restr 0.083 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4598 Nucleic Acid Atoms Solvent Atoms 745 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing