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Crystal structure of native PLL lectin from Photorhabdus luminescens at 1.65 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 290 0.1 M Tris-HCl, 10% PEG 4000, 0.2 M CaCl2, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.96 58.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.12 α = 90 b = 87.677 β = 90 c = 157.691 γ = 90
Symmetry Space Group I 2 2 2
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 PSI PILATUS 6M 2013-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.005 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 76.75 99.7 0.048 36.2 13.5 59360
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 99.1 0.154 14.4 13.7
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 SAD THROUGHOUT 1.65 39.15 56352 3001 99.6 0.14158 0.14063 0.1531 0.15894 0.1694 RANDOM 14.117
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] 0.28 0.07 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.512 r_dihedral_angle_4_deg 15.513 r_dihedral_angle_3_deg 11.615 r_dihedral_angle_1_deg 7.783 r_long_range_B_refined 5.874 r_long_range_B_other 5.563 r_scangle_other 3.882 r_scbond_it 2.821 r_scbond_other 2.812 r_mcangle_it 2.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.512 r_dihedral_angle_4_deg 15.513 r_dihedral_angle_3_deg 11.615 r_dihedral_angle_1_deg 7.783 r_long_range_B_refined 5.874 r_long_range_B_other 5.563 r_scangle_other 3.882 r_scbond_it 2.821 r_scbond_other 2.812 r_mcangle_it 2.762 r_mcangle_other 2.762 r_angle_refined_deg 2.397 r_mcbond_it 1.952 r_mcbond_other 1.95 r_angle_other_deg 1.244 r_chiral_restr 0.169 r_bond_refined_d 0.068 r_gen_planes_refined 0.014 r_bond_other_d 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2743 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing SHELXDE phasing