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Photorhabdus laumondii lectin PLL2 in complex with D-glucose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 8% PEG 4000, 150 mM sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.64 53.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.498 α = 90 b = 71.099 β = 103.95 c = 86.221 γ = 90
Symmetry Space Group I 1 2 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 1.8 47.39 99 0.288 0.903 3.4 3.8 35262 13.025
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 1.8 1.9 98.8 1.045 0.452 1.5 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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 45.64 33419 1672 98.37 0.21156 0.21037 0.23497 0.2422 RANDOM 15.456
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] 0.31 1.05 -0.81 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.45 r_dihedral_angle_3_deg 12.008 r_dihedral_angle_1_deg 7.746 r_dihedral_angle_4_deg 7.093 r_long_range_B_refined 3.403 r_long_range_B_other 3.052 r_angle_other_deg 2.388 r_angle_refined_deg 1.192 r_mcangle_it 0.652 r_mcangle_other 0.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.45 r_dihedral_angle_3_deg 12.008 r_dihedral_angle_1_deg 7.746 r_dihedral_angle_4_deg 7.093 r_long_range_B_refined 3.403 r_long_range_B_other 3.052 r_angle_other_deg 2.388 r_angle_refined_deg 1.192 r_mcangle_it 0.652 r_mcangle_other 0.652 r_scangle_other 0.606 r_mcbond_it 0.385 r_mcbond_other 0.383 r_scbond_it 0.369 r_scbond_other 0.369 r_chiral_restr 0.042 r_bond_other_d 0.037 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_refined_d 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2616 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing