☰ Navigation Tabs
LecB from PA01 in complex with synthetic beta - fucosylamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GZT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 26% Peg6K 1M LiCl 0.1M sodium acetate pH 4.5
3 minutes soaking in 32% Peg Smear Low 50 mM sodium acetate pH 4.5 and 10mM ligand
Crystal Properties Matthews coefficient Solvent content 4.03 69.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.019 α = 90 b = 80.16 β = 109.607 c = 52.429 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 EIGER X 16M 2024-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565 SOLEIL PROXIMA 1
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 1.739 49.39 99.2 0.14 0.172 0.099 0.994 7.6 5.2 40572
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.77 0.815 0.584 0.678 4.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.739 49.389 40572 2073 99.127 0.15 0.1474 0.1606 0.1878 0.1991 11.841
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] -0.138 -0.388 2.412 -1.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.741 r_dihedral_angle_6_deg 14.585 r_dihedral_angle_3_deg 10.623 r_dihedral_angle_1_deg 6.862 r_lrange_it 4.902 r_lrange_other 4.376 r_scangle_it 3.46 r_scangle_other 3.46 r_scbond_it 2.38 r_scbond_other 2.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.741 r_dihedral_angle_6_deg 14.585 r_dihedral_angle_3_deg 10.623 r_dihedral_angle_1_deg 6.862 r_lrange_it 4.902 r_lrange_other 4.376 r_scangle_it 3.46 r_scangle_other 3.46 r_scbond_it 2.38 r_scbond_other 2.379 r_mcangle_it 1.769 r_mcangle_other 1.768 r_angle_refined_deg 1.692 r_mcbond_it 1.33 r_mcbond_other 1.33 r_angle_other_deg 0.638 r_nbd_other 0.255 r_nbd_refined 0.224 r_symmetry_nbd_other 0.212 r_symmetry_xyhbond_nbd_other 0.196 r_symmetry_nbd_refined 0.187 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.143 r_ncsr_local_group_1 0.1 r_chiral_restr 0.099 r_ncsr_local_group_6 0.095 r_ncsr_local_group_5 0.094 r_ncsr_local_group_4 0.093 r_symmetry_nbtor_other 0.09 r_ncsr_local_group_2 0.09 r_ncsr_local_group_3 0.088 r_metal_ion_refined 0.069 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3308 Nucleic Acid Atoms Solvent Atoms 551 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing