3OYF

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI L-870,810


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
3.9168.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159.34α = 90
b = 159.34β = 90
c = 123.26γ = 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
12.5138.64696.10.110.35.252243-3-3
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)
2.512.6592.80.8690.8691.64.97263

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 3OYB2.5138.6552095265695.310.210.20580.20440.232RANDOM52.2761
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]
1.331.33-2.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.309
r_dihedral_angle_4_deg18.32
r_dihedral_angle_3_deg15.459
r_dihedral_angle_1_deg6.195
r_scangle_it3.011
r_scbond_it1.783
r_angle_refined_deg1.515
r_mcangle_it1.387
r_mcbond_it0.719
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.309
r_dihedral_angle_4_deg18.32
r_dihedral_angle_3_deg15.459
r_dihedral_angle_1_deg6.195
r_scangle_it3.011
r_scbond_it1.783
r_angle_refined_deg1.515
r_mcangle_it1.387
r_mcbond_it0.719
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4356
Nucleic Acid Atoms732
Solvent Atoms272
Heterogen Atoms69

Software

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