1MFQ

Crystal Structure Analysis of a Ternary S-Domain Complex of Human Signal Recognition Particle


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L9APDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain)
experimental modelPDB 1JIDPDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain)
experimental modelPDB 1QB2PDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5300.514% (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 coefficientSolvent content
3.6866.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.18α = 90
b = 131.18β = 90
c = 204.051γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9393ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.15099.70.11724.316.619354-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.13.211000.6026.215.91886

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUTPDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain)3.149.631930999299.40.2290.267RANDOM97.6
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]
-12.724.68-12.7225.45
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d16.5
c_scangle_it8.28
c_mcangle_it6.52
c_scbond_it4.68
c_mcbond_it3.68
c_improper_angle_d1.26
c_angle_deg1.1
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1726
Nucleic Acid Atoms2751
Solvent Atoms19
Heterogen Atoms7

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement