3HSL

The Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi's Sarcoma-Associated Herpesvirus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42951.75 M (NH4)2SO4, 100 mM Tris pH 7.4, and 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.8556.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.83α = 90
b = 57.83β = 90
c = 386.1γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 3152008-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97918APS24-ID-E

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
12.85099.70.106209.61052610495
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.80.5426.69.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.83010495989450099.840.268270.26680.29707RANDOM25.034
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]
1.770.891.77-2.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.479
r_dihedral_angle_4_deg13.172
r_dihedral_angle_3_deg10.187
r_scangle_it2.186
r_angle_refined_deg1.956
r_dihedral_angle_1_deg1.788
r_mcangle_it1.362
r_scbond_it1.289
r_mcbond_it0.704
r_chiral_restr0.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.479
r_dihedral_angle_4_deg13.172
r_dihedral_angle_3_deg10.187
r_scangle_it2.186
r_angle_refined_deg1.956
r_dihedral_angle_1_deg1.788
r_mcangle_it1.362
r_scbond_it1.289
r_mcbond_it0.704
r_chiral_restr0.146
r_bond_refined_d0.011
r_gen_planes_refined0.001
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 Atoms2137
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing