3L2R

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DLRPDB ENTRIES 3DLR; 1EX4 CHAIN A RESIDUES 223-266; 7bp B-DNA
experimental modelPDB 1EX4PDB ENTRIES 3DLR; 1EX4 CHAIN A RESIDUES 223-266; 7bp B-DNA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52911.35M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50mM Mes-NaOH, pH 6.5, vapor diffusion, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.968.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.48α = 90
b = 158.48β = 90
c = 124.19γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORADSC2009-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9796DiamondI02

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
12.8838.99999.20.126.33597235972-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.883.04100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 3DLR; 1EX4 CHAIN A RESIDUES 223-266; 7bp B-DNA2.8838.99934156177798.960.203050.202020.22232RANDOM74.31
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]
1.561.56-3.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.294
r_dihedral_angle_4_deg19.042
r_dihedral_angle_3_deg18.24
r_dihedral_angle_1_deg6.434
r_scangle_it2.701
r_angle_refined_deg1.657
r_scbond_it1.591
r_mcangle_it1.062
r_mcbond_it0.538
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.294
r_dihedral_angle_4_deg19.042
r_dihedral_angle_3_deg18.24
r_dihedral_angle_1_deg6.434
r_scangle_it2.701
r_angle_refined_deg1.657
r_scbond_it1.591
r_mcangle_it1.062
r_mcbond_it0.538
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4150
Nucleic Acid Atoms732
Solvent Atoms12
Heterogen Atoms34

Software

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