Navigation Tabs Joint X-ray/neutron room temperature structure of perdeuterated LecA lectin in complex with deuterated galactose
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 Buffer Composition (prepared in D2O instead of H2O):16% PEG 6000,1 M LiCl,0.1 M sodium acetate, pD 5
Initial Sitting Drop Setup:
Mixed 20 uL of a protein solution containing:
9.6 mg/mL perdeuterated LecA, 5 mM Gal-d10, 5 uM calcium chloride (CaCl2),all dissolved in D2O.
With 20 uL of the well solution.
Crystal Growth & Feeding Process:
Crystals initially appeared after 1 week.
To promote further growth, the crystal was fed three times, each time with 5 uL of a pre-equilibrated drop prepared under the same conditions.
Each feeding occurred one week apart, starting one week after initial crystal formation.
This feeding strategy increased the crystal volume from 0.08 mm3 to 0.74 mm3.
Crystal Properties Matthews coefficient Solvent content 2.21 44.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.799 α = 90 b = 106.522 β = 94.634 c = 83.303 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 291 PIXEL DECTRIS PILATUS 6M 2024-10-07 M SINGLE WAVELENGTH 2 1 neutron 291 IMAGE PLATE LADI III 2024-07-08 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.92 ESRF BM07 2 NUCLEAR REACTOR ILL BEAMLINE LADI III 2.8-3.8 ILL LADI III
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.49 44.83 98.8 0.09 0.111 0.998 13 5.4 142031 2 1.9 45.9 72.1 0.243 0.206 0.125 6.1 3.1 50313
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.52 1.688 1.227 0.725 0.9 5.3 2 1.9 2 0.423 0.209 2.4
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.49 41.52 1.35 141805 3972 98.68 0.1581 0.1572 0.1573 0.1851 0.1849 31.74 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.9 45.9 50313 72.1 0.215 0.278
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.8908 f_angle_d 1.6991 f_chiral_restr 0.1135 f_bond_d 0.0138 f_plane_restr 0.0113
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7208 Nucleic Acid Atoms Solvent Atoms 833 Heterogen Atoms 104
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement LAUEGEN data reduction LSCALE data scaling
