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Crystal Structure Analysis of a Ternary S-Domain Complex of Human Signal Recognition Particle
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L9A PDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain) experimental model PDB 1JID PDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain) experimental model PDB 1QB2 PDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 300.5 14% (w/v) PEG8000, 100mM Na-cacodylate, 400mM lithium sulfate, 80mM magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300.5K
Crystal Properties Matthews coefficient Solvent content 3.68 66.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.18 α = 90 b = 131.18 β = 90 c = 204.051 γ = 120
Symmetry Space Group P 65 2 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 CCD ADSC QUANTUM 4 2002-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.1 50 99.7 0.117 24.3 16.6 19354 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.1 3.21 100 0.602 6.2 15.9 1886
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT PDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain) 3.1 49.63 19309 992 99.4 0.229 0.2276 0.267 0.2341 RANDOM 97.6
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] -12.72 4.68 -12.72 25.45
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 16.5 c_scangle_it 8.28 c_mcangle_it 6.52 c_scbond_it 4.68 c_mcbond_it 3.68 c_improper_angle_d 1.26 c_angle_deg 1.1 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1726 Nucleic Acid Atoms 2751 Solvent Atoms 19 Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing CNS refinement