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Co-crystal structure of Carbomycin A bound to the 50S ribosomal subunit of Haloarcula marismortui
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JJ2 1JJ2 native 50S subunit
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 292 PEG 6K, KCl, NH4Cl, KOAc MgCl2, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.17 61.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 212.902 α = 90 b = 300.474 β = 90 c = 575.176 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 2000-09-27 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 3 50 99.2 0.136 0.136 14.2 7.2 370864 367880 -3 -3 44
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) 2.98 3.09 94.8 0.816 0.816 2 34384 36270
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 native 50S subunit 3 20 364257 339428 3311 93.3 0.227 0.227 0.227 0.2152 0.265 RANDOM same r-free set as 1JJ2 58.6
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] 7.62 -1.81 -5.81
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17.7 c_scangle_it 2 c_mcangle_it 1.82 c_improper_angle_d 1.62 c_angle_deg 1.4 c_scbond_it 1.25 c_mcbond_it 1.04 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17.7 c_scangle_it 2 c_mcangle_it 1.82 c_improper_angle_d 1.62 c_angle_deg 1.4 c_scbond_it 1.25 c_mcbond_it 1.04 c_bond_d 0.009 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 61617 Solvent Atoms 7850 Heterogen Atoms 292
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing