3S3M

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and Dolutegravir (S/GSK1349572)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52911.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.9668.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.14α = 90
b = 160.14β = 90
c = 123.43γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91730DiamondI04-1

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
12.4939.14898.70.06725.35569055690-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.492.6299.50.6910.6911.15.58116

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3OYB2.4939.1485663655629283298.330.210.20740.2060.2323RANDOM59.5799
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]
1.121.12-2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.686
r_dihedral_angle_4_deg18.706
r_dihedral_angle_3_deg15.54
r_dihedral_angle_1_deg6.17
r_scangle_it3.014
r_scbond_it1.815
r_angle_refined_deg1.48
r_mcangle_it1.41
r_mcbond_it0.745
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.686
r_dihedral_angle_4_deg18.706
r_dihedral_angle_3_deg15.54
r_dihedral_angle_1_deg6.17
r_scangle_it3.014
r_scbond_it1.815
r_angle_refined_deg1.48
r_mcangle_it1.41
r_mcbond_it0.745
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4375
Nucleic Acid Atoms732
Solvent Atoms235
Heterogen Atoms76

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
PHASERphasing