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2.9 A crystal structure of Streptomycin RNA-aptamer complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NTA Barium form of streptomycin RNA-aptamer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 MES buffer, Magnesium cloride, sodium cloride, MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.29 62.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.634 α = 90 b = 82.634 β = 90 c = 49.153 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2002-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.85 25 99.8 0.045 9.3 3942
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.85 2.95 99.8 0.45
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 Barium form of streptomycin RNA-aptamer 2.9 20 3394 349 99.84 0.20847 0.20373 0.2969 0.25507 0.317 RANDOM 45.528
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] 0.51 0.51 -1.02
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.746 r_angle_other_deg 1.71 r_scangle_it 1.372 r_scbond_it 0.853 r_chiral_restr 0.412 r_nbd_other 0.227 r_symmetry_vdw_other 0.225 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.149
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.746 r_angle_other_deg 1.71 r_scangle_it 1.372 r_scbond_it 0.853 r_chiral_restr 0.412 r_nbd_other 0.227 r_symmetry_vdw_other 0.225 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.149 r_symmetry_vdw_refined 0.123 r_nbtor_other 0.11 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other r_mcbond_it r_mcangle_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 842 Solvent Atoms 6 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing