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Crystal structure of SusDdex (BT3089) with bound IMO5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GCZ Used previously solved BT3089 structure for MR, which was originally solved by PDB 6GCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 0.2M Lithium sulfate
0.1M Sodium acetate pH 4.5
50% w/v PEG 400
Soaked ~10 mM dextran 1.5 into grown crystals (1 crystal per drop), which cracked the large crystal. This was one fragment harvested for the synchrotron.
Crystal Properties Matthews coefficient Solvent content 2.97 58.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87 α = 90 b = 106.15 β = 90 c = 138.34 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 EIGER2 XE 16M 2021-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97960 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.7 67.29 100 0.096 0.1 0.028 1 19.4 25.3 70548
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.73 100 3.015 3.129 0.832 0.587 1.3 27.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 67.288 70548 3544 99.991 0.166 0.1647 0.1647 0.191 0.1909 35.229
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] -1.001 0.457 0.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.3 r_dihedral_angle_3_deg 12.773 r_lrange_it 7.354 r_dihedral_angle_2_deg 7.255 r_scangle_it 6.437 r_dihedral_angle_1_deg 6.396 r_scbond_it 4.788 r_mcangle_it 3.876 r_mcbond_it 2.91 r_angle_refined_deg 2.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.3 r_dihedral_angle_3_deg 12.773 r_lrange_it 7.354 r_dihedral_angle_2_deg 7.255 r_scangle_it 6.437 r_dihedral_angle_1_deg 6.396 r_scbond_it 4.788 r_mcangle_it 3.876 r_mcbond_it 2.91 r_angle_refined_deg 2.075 r_nbtor_refined 0.318 r_nbd_refined 0.21 r_symmetry_nbd_refined 0.183 r_chiral_restr 0.141 r_xyhbond_nbd_refined 0.12 r_symmetry_xyhbond_nbd_refined 0.064 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3645 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling MOLREP phasing Coot model building BUSTER refinement PHASER phasing BUCCANEER model building