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Crystal structure of apo SusDdex (BT3089)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GCZ Used previous BT3089 structure for MR that was itself solved by PDB 6GCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.1M Citric acid pH 5
0.8M ammonium sulphate
Cryoprotected in 3.5M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.94 58.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.5 α = 90 b = 119.5 β = 90 c = 176.98 γ = 90
Symmetry Space Group P 42 21 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 1.65 53.44 100 0.147 0.15 0.029 1 19.3 50.9 153600
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) 1.65 1.68 100 4.128 4.209 0.816 0.833 1 51
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 1.65 53.44 153513 7727 99.993 0.182 0.1804 0.1808 0.2057 0.2059 29.795
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] 0.858 0.858 -1.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.664 r_dihedral_angle_3_deg 12.336 r_lrange_it 8.388 r_dihedral_angle_2_deg 6.503 r_dihedral_angle_1_deg 6.209 r_scangle_it 5.525 r_scbond_it 3.949 r_mcangle_it 2.732 r_mcbond_it 2.166 r_angle_refined_deg 2.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.664 r_dihedral_angle_3_deg 12.336 r_lrange_it 8.388 r_dihedral_angle_2_deg 6.503 r_dihedral_angle_1_deg 6.209 r_scangle_it 5.525 r_scbond_it 3.949 r_mcangle_it 2.732 r_mcbond_it 2.166 r_angle_refined_deg 2.077 r_nbtor_refined 0.317 r_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.14 r_chiral_restr 0.139 r_symmetry_nbd_refined 0.137 r_xyhbond_nbd_refined 0.135 r_ncsr_local_group_1 0.057 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7394 Nucleic Acid Atoms Solvent Atoms 1240 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building Aimless data scaling MOLREP phasing