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RNA duplex with 2-MeImpG analogue bound-3 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 0.04 M Lithium chloride,
0.08 M Strontium chloride hexahydrate
0.04 M Sodium cacodylate trihydrate pH 7.0
30% v/v (+/-)-2-Methyl-2,4-pentanediol,
0.012 M Spermine tetrahydrochloride,
0.02 M Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.48 50.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.229 α = 90 b = 42.229 β = 90 c = 40.098 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 MARMOSAIC 300 mm CCD 2015-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1 ALS 8.2.1
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 1.6 50 99.5 0.083 0.067 23.54 8.9 5712
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 1.6 1.66 94.9 0.364 0.19 0.988 2.41 4.1
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 1.6 40.1 5435 274 99.48 0.17668 0.17431 0.185 0.22601 0.219 RANDOM 24.074
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 0.02
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.487 r_long_range_B_other 4.453 r_scangle_other 4.176 r_angle_other_deg 3.931 r_angle_refined_deg 2.937 r_scbond_it 2.775 r_scbond_other 2.771 r_chiral_restr 0.129 r_bond_other_d 0.077 r_bond_refined_d 0.024
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.487 r_long_range_B_other 4.453 r_scangle_other 4.176 r_angle_other_deg 3.931 r_angle_refined_deg 2.937 r_scbond_it 2.775 r_scbond_other 2.771 r_chiral_restr 0.129 r_bond_other_d 0.077 r_bond_refined_d 0.024 r_gen_planes_refined 0.024 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 276 Solvent Atoms 31 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing