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Human herpesvirus-8 gH/gL in complex with EphA2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HEI 3HEI, 3PHF experimental model PDB 3PHF 3HEI, 3PHF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 0.1M Na-malonate pH 5, 14.2% PEG 3350 , 14 mM adenosine-5'-triphosphate disodium salt hydrate
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.94 α = 90 b = 129 β = 90 c = 267.69 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER X 16M 2020-02-07 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1 2 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9876 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.69 46.44 99.6 0.998 7.9 13.6 35358 76.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.83 0.596
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 3HEI, 3PHF 2.69 46.44 1.33 35282 1762 99.57 0.2247 0.2226 0.2274 0.2649 0.2644 76.67
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 13.812 f_angle_d 0.5343 f_chiral_restr 0.0419 f_plane_restr 0.0041 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7082 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 98
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX phasing PHENIX refinement BUSTER refinement PHENIX model building Coot model building