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Structure of the Thermus thermophilus 30S ribosomal subunit in complex with de-6-MSA-pactamycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277.15 100 mM Mes-KOH (pH 6.5), 200 mM KCl, 75 mM NH4Cl, 15 mM MgCl2, and 26% (vol/vol) 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 4.64 73.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 401 α = 90 b = 401 β = 90 c = 176 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.99 Diamond I04
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 3.1 29.7 91.4 234683 234683
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.2 95.1 0.691 1.47
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 (All) 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 PDB ENTRY 15JE 3.1 29.67 234682 234682 11726 91.35 0.1873 0.1873 0.1852 0.1875 0.2262 0.2242 RANDOM 83.2593
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.871 r_dihedral_angle_3_deg 23.112 r_dihedral_angle_4_deg 20.012 r_mcangle_it 10.609 r_dihedral_angle_1_deg 8.601 r_mcbond_it 6.718 r_mcbond_other 6.718 r_angle_refined_deg 1.751 r_angle_other_deg 1.26 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.871 r_dihedral_angle_3_deg 23.112 r_dihedral_angle_4_deg 20.012 r_mcangle_it 10.609 r_dihedral_angle_1_deg 8.601 r_mcbond_it 6.718 r_mcbond_other 6.718 r_angle_refined_deg 1.751 r_angle_other_deg 1.26 r_chiral_restr 0.101 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19120 Nucleic Acid Atoms 32485 Solvent Atoms Heterogen Atoms 427
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHENIX phasing