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Crystal Structure of Banana Lectin In-complex with Fucose at 2.95 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BMY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.25 293 1.275 M AMMONIUM SULFATE, 30 mM CADMIUM CHLORIDE, 100 mM TRIS-HCl, PH=8.25
Crystal Properties Matthews coefficient Solvent content 4.85 74.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.219 α = 90 b = 81.219 β = 90 c = 147.315 γ = 120
Symmetry Space Group P 32 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 Bruker PHOTON II 2022-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.95 16.96 99.7 0.144 0.203 0.953 9.2 1.9 12279 30
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 2.95 0.422 0.596 0.72 2.4
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 (All) 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 2BMY 2.95 16.956 12270 630 99.232 0.196 0.1923 0.1923 0.2531 0.2531 RANDOM 28.039
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] 0.268 0.134 0.268 -0.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.845 r_dihedral_angle_6_deg 16.194 r_dihedral_angle_1_deg 9.666 r_lrange_other 9.146 r_lrange_it 9.139 r_dihedral_angle_2_deg 7.802 r_scangle_it 5.229 r_scangle_other 5.156 r_mcangle_it 3.632 r_mcangle_other 3.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.845 r_dihedral_angle_6_deg 16.194 r_dihedral_angle_1_deg 9.666 r_lrange_other 9.146 r_lrange_it 9.139 r_dihedral_angle_2_deg 7.802 r_scangle_it 5.229 r_scangle_other 5.156 r_mcangle_it 3.632 r_mcangle_other 3.631 r_scbond_it 3.125 r_scbond_other 3.079 r_mcbond_it 2.13 r_mcbond_other 2.129 r_angle_refined_deg 1.427 r_angle_other_deg 0.431 r_nbd_other 0.223 r_symmetry_nbd_other 0.208 r_nbd_refined 0.198 r_symmetry_nbd_refined 0.193 r_nbtor_refined 0.19 r_symmetry_xyhbond_nbd_refined 0.182 r_xyhbond_nbd_refined 0.172 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.05 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2046 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement PROTEUM data collection Aimless data scaling MOLREP phasing PROTEUM PLUS data reduction