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Crystal structure of the Class V GTP aptamer in complex with GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 methylpentanediol, potasium chloride, manganese chloride, spermine, cacodylate
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.268 α = 90 b = 127.216 β = 90.455 c = 68.368 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 100 PIXEL DECTRIS EIGER X 16M 2023-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.892 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.5 20.001 97.32 0.0897 0.0374 11.23 6.8 30103
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 0.877 0.75
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 SAD FREE R-VALUE 2.5 20.001 30100 1530 97.317 0.202 0.2003 0.2009 0.2378 0.2397 79.848
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] 0.544 0.297 -1.656 1.108
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 10.524 r_lrange_other 10.518 r_scangle_it 8.348 r_scangle_other 8.348 r_scbond_it 5.718 r_scbond_other 5.718 r_angle_refined_deg 1.873 r_angle_other_deg 0.531 r_dihedral_angle_other_2_deg 0.401 r_nbd_refined 0.396
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 10.524 r_lrange_other 10.518 r_scangle_it 8.348 r_scangle_other 8.348 r_scbond_it 5.718 r_scbond_other 5.718 r_angle_refined_deg 1.873 r_angle_other_deg 0.531 r_dihedral_angle_other_2_deg 0.401 r_nbd_refined 0.396 r_symmetry_xyhbond_nbd_refined 0.302 r_nbtor_refined 0.245 r_xyhbond_nbd_refined 0.243 r_nbd_other 0.23 r_symmetry_nbd_other 0.21 r_symmetry_nbd_refined 0.139 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.068 r_ncsr_local_group_6 0.049 r_ncsr_local_group_1 0.045 r_ncsr_local_group_3 0.042 r_ncsr_local_group_4 0.038 r_ncsr_local_group_5 0.038 r_ncsr_local_group_2 0.037 r_metal_ion_refined 0.019 r_gen_planes_refined 0.013 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 5752 Solvent Atoms 74 Heterogen Atoms 276
Software Software Software Name Purpose REFMAC refinement PHENIX refinement Coot model building PHASER phasing Aimless data scaling pointless data scaling XDS data reduction