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Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with GalNAc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 293
Crystal Properties Matthews coefficient Solvent content 3.06 59.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.354 α = 90 b = 86.111 β = 90 c = 129.023 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 DECTRIS PILATUS 6M 2013-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.915 ESRF ID29
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 2.7 47.15 81.7 0.111 6.4 3.1 7221
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 2.7 2.83 84.8 0.394 2.3 3.2
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 THROUGHOUT 2.7 47.15 7217 355 80.5 0.207 0.205 0.244 0.2423 RANDOM 38.92
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] -0.63 1.37 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.607 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_4_deg 13.007 r_dihedral_angle_1_deg 6.274 r_sphericity_bonded 4.804 r_rigid_bond_restr 2.837 r_mcangle_it 2.763 r_mcbond_it 2.176 r_mcbond_other 2.161 r_angle_refined_deg 1.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.607 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_4_deg 13.007 r_dihedral_angle_1_deg 6.274 r_sphericity_bonded 4.804 r_rigid_bond_restr 2.837 r_mcangle_it 2.763 r_mcbond_it 2.176 r_mcbond_other 2.161 r_angle_refined_deg 1.396 r_angle_other_deg 0.767 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1806 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction PHASER phasing MOSFLM data reduction