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RNA duplex with 2-MeImpG analogue bound-2 binding sites
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 10% MPD, 0.040 M sodium cacodylate pH7.0, 0.012 M spermine tetrahydrochloride, 0.08 M sodium chloride, 0.02 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.56 52.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.388 α = 90 b = 43.388 β = 90 c = 253.851 γ = 120
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 ADSC QUANTUM 315 2016-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.5 100 99.4 0.041 0.045 35.37 6.3 15290
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.9 0.575 0.5 0.804 1.84 5.6
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 5HBX 1.5 84.62 14527 763 99.29 0.23892 0.23739 0.2427 0.27019 0.2776 RANDOM 36.469
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.894 r_long_range_B_other 12.893 r_scangle_other 7.061 r_scbond_it 4.482 r_scbond_other 4.48 r_angle_other_deg 4.153 r_angle_refined_deg 2.963 r_chiral_restr 0.119 r_bond_other_d 0.055 r_bond_refined_d 0.027
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.894 r_long_range_B_other 12.893 r_scangle_other 7.061 r_scbond_it 4.482 r_scbond_other 4.48 r_angle_other_deg 4.153 r_angle_refined_deg 2.963 r_chiral_restr 0.119 r_bond_other_d 0.055 r_bond_refined_d 0.027 r_gen_planes_refined 0.022 r_gen_planes_other 0.003 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 594 Solvent Atoms 50 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing