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Crystal structure of E.coli ribosomal protein S2 in complex with N-terminal domain of S1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QBF PDB entries 2qbf and 2oce experimental model PDB 2OCE PDB entries 2qbf and 2oce
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 295.15 0.1 M HEPES-KOH, pH 7.4, 3 mM MgCl2, 7.5% w/v PEG 6000, 3% w/v 2-methyl-pentanediol-2,4, 100 mM KCl
Crystal Properties Matthews coefficient Solvent content 3.03 59.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.28 α = 90 b = 87.28 β = 90 c = 94.36 γ = 120
Symmetry Space Group P 31 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 100 PIXEL DECTRIS PILATUS 6M-F 2012-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.3 37.79 99 0.175 0.063 0.993 7.4 8.1 18726 32.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 91.3 1.106 0.543 0.548 1.5 4.5 1670
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 (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 FREE R-VALUE PDB entries 2qbf and 2oce 2.3 37.79 1.33 18587 949 98.34 0.1668 0.1636 0.1724 0.2287 0.2303 Random selection 42.5864
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.995 f_angle_d 1.09 f_chiral_restr 0.043 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2375 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction PDB_EXTRACT data extraction PHENIX refinement BALBES phasing Aimless data scaling XSCALE data reduction