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Crystal structure of the truncated EBV BFRF1-BFLF2 nuclear egress complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 The protein was dissolved in a buffer consisting of 50 mM TrisHCl, 150 mM NaCl, pH 7.5 and concentrated to values between 10-15 mg/ml. Diffraction quality crystals of BFRF1::BFLF2 were obtained at 4 degree C with 0.2 M sodium malonate, pH 4.5, 20% PEG 3350 as a reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.59 52.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.313 α = 90 b = 59.313 β = 90 c = 265.37 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 100 PIXEL DECTRIS PILATUS3 2M 2017-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.558 47.9 59.64 0.1008 1 17.9 38 40577 26.994976906
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.561 1.617 3.18 0.2287 0.092
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 5d5n 1.55862788727 44.2283333333 1.3436469259 24230 1869 59.3596119454 0.214352796112 0.212026020632 0.2172 0.24198114802 0.2449 50.0140751116
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 13.3587712454 f_angle_d 0.787713411869 f_chiral_restr 0.0477486327389 f_bond_d 0.00733533486113 f_plane_restr 0.00516710950215
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1715 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing