3OYA

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and raltegravir at 2.65 resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OYBPDB entry 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
3.9668.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159.755α = 90
b = 159.755β = 90
c = 124.139γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORADSC2010-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.98011SOLEILPROXIMA 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
12.64638.01999.30.0978.13.746986-3-3
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)
2.652.7999.20.8560.8561.63.66741

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB entry 3OYB2.6538.0246802235998.880.210.20640.20520.2282RANDOM55.6999
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]
1.221.22-2.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.509
r_dihedral_angle_4_deg17.239
r_dihedral_angle_3_deg15.971
r_dihedral_angle_1_deg5.982
r_scangle_it2.988
r_scbond_it1.744
r_angle_refined_deg1.556
r_mcangle_it1.361
r_mcbond_it0.709
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.509
r_dihedral_angle_4_deg17.239
r_dihedral_angle_3_deg15.971
r_dihedral_angle_1_deg5.982
r_scangle_it2.988
r_scbond_it1.744
r_angle_refined_deg1.556
r_mcangle_it1.361
r_mcbond_it0.709
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4362
Nucleic Acid Atoms732
Solvent Atoms234
Heterogen Atoms71

Software

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