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Crystal structurel of FleA lectin in complex with a monovalent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 50 mM L-Arginin, 50 mm L-Glutamate, 28% PEG Smear Broad and 5% glycerol (BCS screen 1-32)
Crystal Properties Matthews coefficient Solvent content 2.19 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.117 α = 103.083 b = 46.893 β = 98.536 c = 80.173 γ = 108.512
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 2018-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 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 1.4 42.54 99.2 0.052 0.061 0.032 0.998 16.1 6.5 115240
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 96.4 0.3 0.388 0.236 0.0963 3.1 4.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4AH4 1.4 42.534 115179 5702 99.132 0.12 0.1185 0.1184 0.1579 0.1578 18.21
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] 0.957 -0.134 0.455 -0.471 -0.199 -0.277
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.277 r_dihedral_angle_4_deg 12.22 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 7.476 r_rigid_bond_restr 3.999 r_lrange_it 3.555 r_lrange_other 3.377 r_scangle_it 3.358 r_scangle_other 3.357 r_scbond_it 2.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.277 r_dihedral_angle_4_deg 12.22 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 7.476 r_rigid_bond_restr 3.999 r_lrange_it 3.555 r_lrange_other 3.377 r_scangle_it 3.358 r_scangle_other 3.357 r_scbond_it 2.891 r_scbond_other 2.891 r_mcangle_other 2.399 r_mcangle_it 2.398 r_mcbond_it 2.104 r_mcbond_other 2.098 r_angle_refined_deg 1.82 r_angle_other_deg 1.565 r_nbd_other 0.237 r_nbd_refined 0.199 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.181 r_symmetry_nbd_refined 0.164 r_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.123 r_symmetry_xyhbond_nbd_refined 0.119 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_1 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4909 Nucleic Acid Atoms Solvent Atoms 713 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing