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Crystal structure of RNA G2C4 repeats - native model pH 6.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 0.08M Magnesium acetate tetrahydrate, 0.05M Sodium cacodylate trihydrate pH 6.5, 30% v/w Polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 1.65 25.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.656 α = 90 b = 45.84 β = 90 c = 51.474 γ = 90
Symmetry Space Group C 2 2 21
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 2024-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.72932 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 0.918 25.75 99.9 0.99 17.2 13.3 34769
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.92 0.97 99.8 0.73 1.59
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 0.918 25.75 34766 1726 99.94 0.119 0.1184 0.1294 0.1361 12.556
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] 0.2 0.05 -0.251
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 8.598 r_angle_refined_deg 2.749 r_angle_other_deg 2.446 r_scangle_it 2.154 r_scangle_other 2.154 r_lrange_it 1.976 r_lrange_other 1.876 r_scbond_it 1.695 r_scbond_other 1.693 r_nbd_refined 0.423
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 8.598 r_angle_refined_deg 2.749 r_angle_other_deg 2.446 r_scangle_it 2.154 r_scangle_other 2.154 r_lrange_it 1.976 r_lrange_other 1.876 r_scbond_it 1.695 r_scbond_other 1.693 r_nbd_refined 0.423 r_symmetry_xyhbond_nbd_refined 0.325 r_xyhbond_nbd_refined 0.272 r_symmetry_nbd_other 0.252 r_nbtor_refined 0.246 r_nbd_other 0.227 r_symmetry_nbd_refined 0.19 r_chiral_restr 0.157 r_symmetry_nbtor_other 0.094 r_metal_ion_refined 0.036 r_gen_planes_refined 0.035 r_gen_planes_other 0.032 r_bond_refined_d 0.019 r_symmetry_xyhbond_nbd_other 0.012 r_symmetry_metal_ion_refined 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 492 Solvent Atoms 128 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing