☰ Navigation Tabs
Photorhabdus laumondii lectin PLL in complex with alpha-methyl-fucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C9L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 277 20 mM Tris/HCl
150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 3.06 59.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.217 α = 90 b = 89.184 β = 90 c = 158.773 γ = 90
Symmetry Space Group I 2 2 2
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 2022-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 45.555 100 0.084 0.024 0.999 18.6 13.5 66905
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 1.6 1.69 100 1.003 0.288 0.828 2.8 12.9
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 1.6 45.555 66903 3371 99.981 0.163 0.1625 0.1764 0.1796 0.1919 18.573
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] 1.048 -0.381 -0.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.746 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_2_deg 8.302 r_dihedral_angle_1_deg 8.068 r_lrange_it 5.151 r_lrange_other 4.995 r_scangle_it 4.015 r_scangle_other 4.014 r_mcangle_other 2.774 r_mcangle_it 2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.746 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_2_deg 8.302 r_dihedral_angle_1_deg 8.068 r_lrange_it 5.151 r_lrange_other 4.995 r_scangle_it 4.015 r_scangle_other 4.014 r_mcangle_other 2.774 r_mcangle_it 2.77 r_scbond_it 2.747 r_scbond_other 2.746 r_mcbond_it 2.021 r_mcbond_other 2.021 r_angle_refined_deg 1.679 r_angle_other_deg 0.618 r_symmetry_nbd_other 0.191 r_nbd_refined 0.184 r_nbtor_refined 0.177 r_nbd_other 0.159 r_symmetry_nbd_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2726 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing