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Photorhabdus laumondii lectin PLL2 in complex with 3-O-methyl-D-glucose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 11% PEG 4000, 150 mM sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.97 37.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.646 α = 90 b = 56.708 β = 95.33 c = 108.477 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 PILATUS3 2M 2018-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.12 44.84 98.6 0.072 0.998 8.1 3.7 224157 7.939
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.15 98.9 0.768 0.74 1.6 3.5
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 (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 THROUGHOUT 1.12 44.84 224157 11786 98.59 0.13766 0.13641 0.1439 0.16099 0.1667 RANDOM 12.321
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] 0.06 -0.78 -0.63 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.174 r_dihedral_angle_4_deg 13.22 r_dihedral_angle_3_deg 10.815 r_dihedral_angle_1_deg 7.961 r_rigid_bond_restr 6.166 r_long_range_B_refined 2.924 r_long_range_B_other 2.156 r_angle_refined_deg 1.575 r_angle_other_deg 1.495 r_scangle_other 1.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.174 r_dihedral_angle_4_deg 13.22 r_dihedral_angle_3_deg 10.815 r_dihedral_angle_1_deg 7.961 r_rigid_bond_restr 6.166 r_long_range_B_refined 2.924 r_long_range_B_other 2.156 r_angle_refined_deg 1.575 r_angle_other_deg 1.495 r_scangle_other 1.327 r_scbond_it 1.07 r_scbond_other 1.07 r_mcangle_it 0.971 r_mcangle_other 0.971 r_mcbond_it 0.793 r_mcbond_other 0.793 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5268 Nucleic Acid Atoms Solvent Atoms 1059 Heterogen Atoms 269
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing