☰ Navigation Tabs
Photorhabdus laumondii lectin PLL4 in complex with alpha-methyl-fucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T96
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 20% PEG4000
20% PEG300
300 mM MgCl2
100 mM MES
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.013 α = 90 b = 82.859 β = 105.357 c = 70.3 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 100 PIXEL DECTRIS EIGER X 16M 2022-10-06 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) 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 1.95 46.28 99.9 0.045 0.048 0.018 0.9999 21.7 6.9 56507
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 1.95 2.06 0.231 0.251 0.098 0.978 6.8
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 1.95 41.464 56484 2799 99.897 0.206 0.2046 0.2121 0.2399 0.246 33.904
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] -1.17 -0.025 2.059 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.319 r_dihedral_angle_3_deg 13.265 r_dihedral_angle_2_deg 9.427 r_dihedral_angle_1_deg 9.289 r_lrange_it 6.559 r_lrange_other 6.549 r_scangle_it 5.411 r_scangle_other 5.41 r_mcangle_other 4.143 r_mcangle_it 4.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.319 r_dihedral_angle_3_deg 13.265 r_dihedral_angle_2_deg 9.427 r_dihedral_angle_1_deg 9.289 r_lrange_it 6.559 r_lrange_other 6.549 r_scangle_it 5.411 r_scangle_other 5.41 r_mcangle_other 4.143 r_mcangle_it 4.142 r_scbond_it 3.726 r_scbond_other 3.726 r_mcbond_it 3.122 r_mcbond_other 3.122 r_angle_refined_deg 1.414 r_angle_other_deg 0.532 r_metal_ion_refined 0.281 r_symmetry_nbd_other 0.203 r_nbd_other 0.193 r_nbtor_refined 0.178 r_nbd_refined 0.177 r_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.086 r_symmetry_nbd_refined 0.076 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_refined 0.051 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5226 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing