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Crystal Structure of O-linked Glycosylated VSG3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Hanging drops formed from mixing a 1:1 volume ratio of the protein with an equilibration buffer consisting of 16-22% polyethylene glycol (PEG) molecular weight 3350 Da, 200-325mM NaCl, and 100mM Tris pH 8.2 (tris(hydroxymethyl)aminomethane)
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.854 α = 90 b = 129.854 β = 90 c = 129.854 γ = 90
Symmetry Space Group I 21 3
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-F 2015-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9194 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.41 91.82 97.9 0.022 0.999 19.1 4.1 68683 19.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.43 73.9 0.725 0.407 0.6 1.6
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 1.41 91.82 64954 3462 97.9 0.13193 0.13003 0.1298 0.16921 0.1692 RANDOM 23.203
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.753 r_sphericity_free 30.247 r_dihedral_angle_4_deg 19.268 r_dihedral_angle_3_deg 12.627 r_sphericity_bonded 11.402 r_dihedral_angle_1_deg 5.247 r_long_range_B_refined 4.604 r_scangle_other 4.332 r_long_range_B_other 4.28 r_scbond_it 3.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.753 r_sphericity_free 30.247 r_dihedral_angle_4_deg 19.268 r_dihedral_angle_3_deg 12.627 r_sphericity_bonded 11.402 r_dihedral_angle_1_deg 5.247 r_long_range_B_refined 4.604 r_scangle_other 4.332 r_long_range_B_other 4.28 r_scbond_it 3.717 r_scbond_other 3.717 r_mcangle_it 3.157 r_mcangle_other 3.156 r_rigid_bond_restr 2.917 r_mcbond_it 2.553 r_mcbond_other 2.553 r_angle_refined_deg 1.758 r_angle_other_deg 1.051 r_chiral_restr 0.121 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2652 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling