3C5D

Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C3Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5310MPD, KCl, MgCl2, Na cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 310K
Crystal Properties
Matthews coefficientSolvent content
2.5151.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.086α = 90
b = 29.294β = 120.84
c = 59.607γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 3152006-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9783ESRFID14-4

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
11.83089.40.04331.24.12428630.7
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)
1.81.8653.10.176.22.61452

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3C3Z1.819.952692624175179689.80.2320.2320.245RANDOM47.2
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]
-8.76-0.615.47-6.71
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d8.2
c_improper_angle_d4.9
c_angle_deg1.2
c_bond_d0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms980
Solvent Atoms140
Heterogen Atoms106

Software

Software
Software NamePurpose
CNSrefinement
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing