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1.5 A X-ray crystal structure of Apramycin complex with RNA fragment GGCGUCGCUAGUACCG/GGUACUAAAAGUCGCCC containing the human ribosomal decoding A site: RNA construct with 3'-overhang
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other STANDARD RNA-MODEL BUILT IN TURBO-FRODO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.05M MES BUFFER, 15-20% MPD, 0.02-0.04M MAGNESIUM ACETATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.31 α = 90 b = 36.693 β = 90 c = 86.679 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 4 2000-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9A 1.0000 NSLS X9A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 20 92.73 13865 13865
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 STANDARD RNA-MODEL BUILT IN TURBO-FRODO 1.51 19.92 13173 13173 692 92.73 0.20006 0.19876 0.211 0.2268 0.204 RANDOM 20.524
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] 0.02 -0.06 0.04
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.535 r_scbond_it 1.873 r_angle_refined_deg 1.793 r_angle_other_deg 1.746 r_chiral_restr 0.871 r_symmetry_hbond_refined 0.247 r_xyhbond_nbd_refined 0.216 r_nbd_other 0.206 r_symmetry_vdw_other 0.203 r_nbd_refined 0.124
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.535 r_scbond_it 1.873 r_angle_refined_deg 1.793 r_angle_other_deg 1.746 r_chiral_restr 0.871 r_symmetry_hbond_refined 0.247 r_xyhbond_nbd_refined 0.216 r_nbd_other 0.206 r_symmetry_vdw_other 0.203 r_nbd_refined 0.124 r_symmetry_vdw_refined 0.112 r_metal_ion_refined 0.065 r_xyhbond_nbd_other 0.05 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbtor_refined r_nbtor_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other 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 698 Solvent Atoms 164 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing