3S3N

Crystal structure of the Prototype Foamy Virus (PFV) S217H mutant intasome in complex with magnesium and Dolutegravir (S/GSK1349572)


X-RAY DIFFRACTION

Starting Model(s)

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

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
3.9668.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.05α = 90
b = 160.05β = 90
c = 123.61γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97630DiamondI02

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
12.4939.15894.90.0972.19.35330053300-3-3
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)
12.492.6296.90.8220.8220.99.17861

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 REPLACEMENTTHROUGHOUT3OYL2.4939.15856595531992720940.210.21060.20950.2318RANDOM60.4868
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]
2.362.36-4.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.772
r_dihedral_angle_4_deg17.679
r_dihedral_angle_3_deg16.601
r_dihedral_angle_1_deg6.156
r_scangle_it2.989
r_scbond_it1.824
r_angle_refined_deg1.598
r_mcangle_it1.45
r_mcbond_it0.757
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.772
r_dihedral_angle_4_deg17.679
r_dihedral_angle_3_deg16.601
r_dihedral_angle_1_deg6.156
r_scangle_it2.989
r_scbond_it1.824
r_angle_refined_deg1.598
r_mcangle_it1.45
r_mcbond_it0.757
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4351
Nucleic Acid Atoms732
Solvent Atoms210
Heterogen Atoms73

Software

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