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1.8 A X-ray crystal structure of Apramycin complex with RNA fragment GGGCGUCGCUAGUACC/CGGUACUAAAAGUCGCC containing the human ribosomal decoding A site: RNA construct with 5'-overhang
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OE5
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 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.1 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.858 α = 90 b = 37.259 β = 90 c = 85.586 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 1.8 20 99.44 8704 8704
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 2OE5 1.8 20 8264 440 99.44 0.20984 0.20836 0.2197 0.23611 0.2233 RANDOM 24.678
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] -1.77 2.83 -1.05
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.546 r_angle_other_deg 1.909 r_scbond_it 1.855 r_angle_refined_deg 1.817 r_chiral_restr 0.623 r_nbd_other 0.22 r_symmetry_vdw_other 0.187 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.147 r_nbd_refined 0.112
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.546 r_angle_other_deg 1.909 r_scbond_it 1.855 r_angle_refined_deg 1.817 r_chiral_restr 0.623 r_nbd_other 0.22 r_symmetry_vdw_other 0.187 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.147 r_nbd_refined 0.112 r_symmetry_vdw_refined 0.098 r_xyhbond_nbd_other 0.05 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.005 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_nbtor_refined r_nbtor_other r_metal_ion_refined 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 151 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing