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Crystal structure of the Hexameric Ring of Epstein-Barr Virus Nuclear Antigen-1, EBNA1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VHI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 Concentrated EBNA1 was diluted 1:1 in a solution containing 50 mM morpholineethanesulfonic acid (MES) (pH 6.5) and 800 mM sodium formate.
Crystal Properties Matthews coefficient Solvent content 1.95 36.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.28 α = 60.01 b = 84.768 β = 87.31 c = 84.709 γ = 88.53
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944+ VariMax optical mirrors 2011-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 1.9 50 82.4 0.063 9.68 1.9 48887
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1VHI 1.9 29.189 0.02 45443 1879 76.46 0.2015 0.1983 0.2105 0.2764 0.283
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.022 f_angle_d 1.599 f_chiral_restr 0.057 f_bond_d 0.015 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6373 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing