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Crystal structure of full-length HPV31 E6 oncoprotein in complex with LXXLL peptide of ubiquitin ligase E6AP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XR8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 200mM tri-lithium citrate, 20% PEG 33350
protein concentration: 30mg/ml
cryo condition: 35% glycerol
Crystal Properties Matthews coefficient Solvent content 2.89 57.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.64 α = 90 b = 113.64 β = 90 c = 185.97 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 PILATUS 2M 2019-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 2.8 49.25 99.1 0.23 0.998 14.49 19.4 18049 62.24
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 2.8 2.87 2.076 0.52 1.57 18.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4XR8 2.8 49.21 1.34 18043 894 99.37 0.2319 0.23 0.2384 0.2682 0.2751 Random selection 85.21
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 16.9201 f_angle_d 0.619 f_chiral_restr 0.0438 f_bond_d 0.0034 f_plane_restr 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4202 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing