3OY9

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with manganese at 2.55 resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L2RPDB entry 3L2R

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
3.9769.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.09α = 90
b = 160.09β = 90
c = 123.94γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORADSC2010-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97950DiamondI02

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
12.5539.20698.90.08414.15.552142-3-3
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)
2.552.69990.9310.93125.47536

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 3L2R2.5539.2152062262798.330.20.19860.19730.2217RANDOM58.3457
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]
1.461.46-2.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.983
r_dihedral_angle_4_deg18.176
r_dihedral_angle_3_deg15.897
r_dihedral_angle_1_deg6.015
r_scangle_it2.99
r_scbond_it1.777
r_angle_refined_deg1.496
r_mcangle_it1.391
r_mcbond_it0.725
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.983
r_dihedral_angle_4_deg18.176
r_dihedral_angle_3_deg15.897
r_dihedral_angle_1_deg6.015
r_scangle_it2.99
r_scbond_it1.777
r_angle_refined_deg1.496
r_mcangle_it1.391
r_mcbond_it0.725
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4339
Nucleic Acid Atoms732
Solvent Atoms274
Heterogen Atoms39

Software

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