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Photorhabdus laumondii lectin PLL2 in complex with alpha-methyl-fucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 100 mM sodium acetate
11% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.42 49.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.16 α = 90 b = 85.676 β = 102.062 c = 68.188 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 PILATUS 6M-F 2018-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9799 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.85 85.68 99.1 0.057 0.066 0.033 0.999 11.4 3.9 64783
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 1.85 1.95 98.5 0.63 0.729 0.363 0.785 2.3 3.9
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 1.85 66.683 64755 3207 98.961 0.198 0.1968 0.2059 0.2296 0.235 33.975
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] -1.132 0.41 2.857 -1.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.379 r_dihedral_angle_3_deg 12.253 r_dihedral_angle_1_deg 7.95 r_dihedral_angle_2_deg 7.71 r_lrange_it 5.976 r_lrange_other 5.969 r_scangle_it 4.639 r_scangle_other 4.638 r_mcangle_other 3.863 r_mcangle_it 3.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.379 r_dihedral_angle_3_deg 12.253 r_dihedral_angle_1_deg 7.95 r_dihedral_angle_2_deg 7.71 r_lrange_it 5.976 r_lrange_other 5.969 r_scangle_it 4.639 r_scangle_other 4.638 r_mcangle_other 3.863 r_mcangle_it 3.862 r_scbond_it 3.22 r_scbond_other 3.22 r_mcbond_it 2.938 r_mcbond_other 2.931 r_angle_refined_deg 1.305 r_angle_other_deg 0.488 r_symmetry_nbd_other 0.193 r_nbd_other 0.193 r_nbd_refined 0.182 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.169 r_symmetry_nbd_refined 0.142 r_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 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 5268 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing