3KTW | pdb_00003ktw

Crystal structure of the SRP19/S-domain SRP RNA complex of Sulfolobus solfataricus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LNGPDB entry 1LNG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.7293100 mM Na cacodylate, 400 mM KCl, 10 mM CaCl2, 15% (w/v) PEG4000, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.5865.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.307α = 90
b = 79.338β = 101.99
c = 114.067γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2006-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.93300ESRFID14-2

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
13.264.799.20.09213.63.92074420578
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)
13.23.3799.20.3883.33.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1LNG3.264.682079420563105498.890.2420.2420.240.230.2850.27RANDOM86.721
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]
-7.56-4.773.61.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.472
r_dihedral_angle_3_deg21.476
r_dihedral_angle_4_deg17.625
r_dihedral_angle_1_deg5.317
r_scangle_it1.95
r_angle_refined_deg1.619
r_scbond_it1.116
r_mcangle_it0.961
r_mcbond_it0.506
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.472
r_dihedral_angle_3_deg21.476
r_dihedral_angle_4_deg17.625
r_dihedral_angle_1_deg5.317
r_scangle_it1.95
r_angle_refined_deg1.619
r_scbond_it1.116
r_mcangle_it0.961
r_mcbond_it0.506
r_chiral_restr0.073
r_gen_planes_refined0.019
r_bond_refined_d0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1537
Nucleic Acid Atoms4106
Solvent Atoms
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing