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RNA duplex bound with GMP and AMP monomers
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C8N PDB entry 6C8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 10% v/v MPD, 0.040 M sodium cacodylate trihydrate, pH 7.0, 0.012 M Spermine tetrahydrochloride, 0.08 M sodium chloride, 0.012 M potassium chloride, 0.02 M magnesium chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.26 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.526 α = 90 b = 43.526 β = 90 c = 80.139 γ = 120
Symmetry Space Group P 3 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 99 CCD MAR CCD 130 mm 2021-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.987 APS 21-ID-F
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 1.45 50 98.5 0.122 0.129 0.042 0.978 121.5 10.7 15931
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 1.45 1.5 100 0.531 0.558 0.169 0.972 7.9 10.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 6C8N 1.45 26.73 15101 789 98.21 0.22118 0.22012 0.2319 0.24181 0.2484 RANDOM 27.869
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_long_range_B_other 4.857 r_long_range_B_refined 4.82 r_angle_other_deg 4.045 r_scangle_other 3.86 r_angle_refined_deg 3.611 r_scbond_it 2.663 r_scbond_other 2.577 r_chiral_restr 0.172 r_bond_refined_d 0.028 r_bond_other_d 0.026
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 4.857 r_long_range_B_refined 4.82 r_angle_other_deg 4.045 r_scangle_other 3.86 r_angle_refined_deg 3.611 r_scbond_it 2.663 r_scbond_other 2.577 r_chiral_restr 0.172 r_bond_refined_d 0.028 r_bond_other_d 0.026 r_gen_planes_refined 0.02 r_gen_planes_other 0.002 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 598 Solvent Atoms 69 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing