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The Structure of a Ribosomal Protein S8/spc Operon mRNA Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J5E PDB entry 1J5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 296 PEG 8000, zinc acetate, sodium acetate buffer, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.26 61.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.22 α = 90 b = 61.22 β = 90 c = 332.52 γ = 120
Symmetry Space Group P 32 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 M SINGLE WAVELENGTH 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0049 NSLS X25 2 SYNCHROTRON NSLS BEAMLINE X25 0.9928 NSLS X25 3 SYNCHROTRON NSLS BEAMLINE X25 1.008998 NSLS X25
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 2.7 50 20950
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 3907
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1J5E 2.7 50 2 19880 1070 99.8 0.23917 0.23734 0.23734 0.2344 0.27313 0.2658 RANDOM 44.626
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.905 r_scangle_it 5.825 r_scbond_it 3.798 r_mcangle_it 3.773 r_angle_refined_deg 2.331 r_mcbond_it 2.187 r_symmetry_vdw_refined 0.316 r_symmetry_hbond_refined 0.288 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.905 r_scangle_it 5.825 r_scbond_it 3.798 r_mcangle_it 3.773 r_angle_refined_deg 2.331 r_mcbond_it 2.187 r_symmetry_vdw_refined 0.316 r_symmetry_hbond_refined 0.288 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1921 Nucleic Acid Atoms 2008 Solvent Atoms 5 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing