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Photorhabdus laumondii lectin PLL5 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 7.5 293 20 mM Tris
150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 3.16 61.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.712 α = 90 b = 102.94 β = 90.028 c = 97.476 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 2019-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.699 45.515 98.8 0.118 0.138 0.069 0.993 6.2 3.8 200282
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 1.7 1.79 0.784 0.917 0.468 0.466 1.6
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 1.699 45.515 200149 10442 98.503 0.183 0.1823 0.1952 0.1997 0.2113 19.253
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] -5.193 1.795 1.938 3.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.857 r_dihedral_angle_3_deg 12.007 r_dihedral_angle_4_deg 10.463 r_dihedral_angle_1_deg 8.535 r_lrange_it 2.277 r_lrange_other 2.207 r_angle_refined_deg 1.262 r_angle_other_deg 1.228 r_mcangle_it 1.223 r_mcangle_other 1.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.857 r_dihedral_angle_3_deg 12.007 r_dihedral_angle_4_deg 10.463 r_dihedral_angle_1_deg 8.535 r_lrange_it 2.277 r_lrange_other 2.207 r_angle_refined_deg 1.262 r_angle_other_deg 1.228 r_mcangle_it 1.223 r_mcangle_other 1.223 r_scangle_it 1.151 r_scangle_other 1.151 r_mcbond_it 0.795 r_mcbond_other 0.795 r_scbond_it 0.761 r_scbond_other 0.761 r_nbd_other 0.213 r_symmetry_nbd_other 0.181 r_nbd_refined 0.17 r_symmetry_nbd_refined 0.166 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_other 0.161 r_xyhbond_nbd_refined 0.12 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.051 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10562 Nucleic Acid Atoms Solvent Atoms 650 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing