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The Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi's Sarcoma-Associated Herpesvirus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 295 1.75 M (NH4)2SO4, 100 mM Tris pH 7.4, and 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.85 56.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.83 α = 90 b = 57.83 β = 90 c = 386.1 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 2008-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 50 99.7 0.106 20 9.6 10526 10495
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 0.542 6.6 9.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.8 30 10495 9894 500 99.84 0.26827 0.2668 0.2522 0.29707 0.2821 RANDOM 25.034
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] 1.77 0.89 1.77 -2.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.479 r_dihedral_angle_4_deg 13.172 r_dihedral_angle_3_deg 10.187 r_scangle_it 2.186 r_angle_refined_deg 1.956 r_dihedral_angle_1_deg 1.788 r_mcangle_it 1.362 r_scbond_it 1.289 r_mcbond_it 0.704 r_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.479 r_dihedral_angle_4_deg 13.172 r_dihedral_angle_3_deg 10.187 r_scangle_it 2.186 r_angle_refined_deg 1.956 r_dihedral_angle_1_deg 1.788 r_mcangle_it 1.362 r_scbond_it 1.289 r_mcbond_it 0.704 r_chiral_restr 0.146 r_bond_refined_d 0.011 r_gen_planes_refined 0.001 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 Atoms Number Protein Atoms 2137 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building REFMAC refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing