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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 8.2 295 18% PEG 3350, 100 mM Tris HCl pH 8.2, 0.2 M lithium
chloride, and 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.3 α = 90 b = 58.3 β = 90 c = 386.92 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 2008-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E .97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 30 95.2 0.095 0.095 18.012 11.1 10612 10103 -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) Redundancy Number Unique Reflections (All) 1 2.8 2.9 62.1 0.492 0.492 2.7 0.049
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 SAD THROUGHOUT 2.81 29.15 10103 9267 465 96.33 0.25311 0.25169 0.2388 0.28131 0.2678 RANDOM 31.36
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] 2.66 1.33 2.66 -3.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.996 r_dihedral_angle_4_deg 13.76 r_dihedral_angle_3_deg 10.093 r_scangle_it 2.522 r_angle_refined_deg 1.839 r_dihedral_angle_1_deg 1.6 r_mcangle_it 1.48 r_scbond_it 1.442 r_mcbond_it 0.764 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.996 r_dihedral_angle_4_deg 13.76 r_dihedral_angle_3_deg 10.093 r_scangle_it 2.522 r_angle_refined_deg 1.839 r_dihedral_angle_1_deg 1.6 r_mcangle_it 1.48 r_scbond_it 1.442 r_mcbond_it 0.764 r_chiral_restr 0.125 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 2145 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building REFMAC refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing