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Co-crystal structure of CCA-Phe-caproic acid-biotin and sparsomycin bound to the 50S ribosomal subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 PEG 6000, NaCl, KCl, NH4Cl, MgCl2, ethylene glycol, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 100K
Crystal Properties Matthews coefficient Solvent content 3.13 60.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.661 α = 90 b = 299.773 β = 90 c = 573.684 γ = 90
Symmetry Space Group C 2 2 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 CUSTOM-MADE 2001-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.033 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.8 50 94.3 0.136 0.136 15 7 442473 416857 -3 49.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 100 0.9 0.9 2 7 44081
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1JJ2 2.8 20 442054 416857 4096 94.3 0.181 0.181 0.181 0.1791 0.222 RANDOM 49.6
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] 6.07 -2.72 -3.35
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 15.6 c_scangle_it 2.19 c_mcangle_it 1.91 c_scbond_it 1.41 c_improper_angle_d 1.39 c_angle_deg 1.1 c_mcbond_it 1.09 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 15.6 c_scangle_it 2.19 c_mcangle_it 1.91 c_scbond_it 1.41 c_improper_angle_d 1.39 c_angle_deg 1.1 c_mcbond_it 1.09 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28801 Nucleic Acid Atoms 61676 Solvent Atoms 7858 Heterogen Atoms 276
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling CNS refinement HKL-2000 data reduction CNS phasing