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Fucose-binding lectin from Burkholderia ambifaria (BamBL) in complex with a fucosyl derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292.15 200 mM trisodium citrate, 100 mM sodium acetate pH 5.0 and 24% PEG 8000, 1% DMSO
Crystal Properties Matthews coefficient Solvent content 2.74 55.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.092 α = 90 b = 49.163 β = 91.36 c = 115.098 γ = 90
Symmetry Space Group I 1 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 PILATUS 6M 2019-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 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 1.65 45.25 98.1 0.088 0.095 0.036 0.999 11.8 6.9 72307
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 1.65 1.68 96.5 1.26 1.36 0.509 0.627 7.1
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 3ZW0 1.65 45.21 68772 3534 98.04 0.1782 0.1767 0.1865 0.2085 0.2168 RANDOM 22.618
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] -0.19 -0.49 -1.27 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.77 r_dihedral_angle_3_deg 11.959 r_dihedral_angle_4_deg 8.986 r_dihedral_angle_1_deg 8.152 r_angle_refined_deg 1.687 r_angle_other_deg 1.495 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.77 r_dihedral_angle_3_deg 11.959 r_dihedral_angle_4_deg 8.986 r_dihedral_angle_1_deg 8.152 r_angle_refined_deg 1.687 r_angle_other_deg 1.495 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3962 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 262
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing