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Crystal structure of PHA-E lectin in complex with bisected glycan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 0.1M sodium acetate (pH 4.5), 25 %(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.21 α = 90 b = 122.838 β = 90.66 c = 97.664 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 95 CCD ADSC QUANTUM 210 2014-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3 100 99.9 0.071 27.1 4.2 45064
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 3 3.05 100 0.32 5.1 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3WCS 3 100 42772 2268 99.78 0.23097 0.2287 0.2292 0.27371 0.2748 RANDOM 42.106
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 -1.31 -1.6 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.834 r_dihedral_angle_3_deg 13.621 r_dihedral_angle_4_deg 8.353 r_dihedral_angle_1_deg 5.559 r_long_range_B_refined 4.566 r_mcangle_it 2.649 r_mcbond_it 1.458 r_scbond_it 1.09 r_angle_refined_deg 1.053 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.834 r_dihedral_angle_3_deg 13.621 r_dihedral_angle_4_deg 8.353 r_dihedral_angle_1_deg 5.559 r_long_range_B_refined 4.566 r_mcangle_it 2.649 r_mcbond_it 1.458 r_scbond_it 1.09 r_angle_refined_deg 1.053 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14656 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 816
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing