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Crystal Structure of the Yeast Ribosomal Protein Rps3 in Complex with its Chaperone Yar1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J00 PDB ENTRY 2J00
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M MES PH 6.0, 200 MM LITHIUM SULPHATE, 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.53 65.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.83 α = 90 b = 104.83 β = 90 c = 95.96 γ = 90
Symmetry Space Group P 42 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 PIXEL DECTRIS PILATUS 6M 2012-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.84 34.57 93.9 0.07 19.85 8.19130646 12331 2 76.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 3.01 94 0.79 2.86 8.41671018
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2J00 2.842 34.574 2 12328 616 94.08 0.1908 0.1891 0.1954 0.2245 0.2237 79.5
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 13.653 f_angle_d 0.915 f_chiral_restr 0.067 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2629 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing