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Crystal structure of a trimeric variant of the Epstein-Barr virus glycoprotein B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GUM PDB entry 2GUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 298 0.1 M N-Cyclohexyl-3-aminopropanesulfonic acid (CAPS) pH 10.5 or 11.5, 1.40 M (NH4)2SO4 (AS) and 0.2 M Li2SO4, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.81 74.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.8 α = 90 b = 106.8 β = 90 c = 210.75 γ = 120
Symmetry Space Group P 3 2 1
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 MAR CCD 165 mm 2007-05-01 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 1.0379 APS 5ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.2 50 98.5 8.3 23367
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 91.6 3 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB entry 2GUM 3.2 26.61 21144 2155 98.36 0.24635 0.24246 0.2377 0.28292 0.2768 RANDOM 79.778
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] 2.79 1.39 2.79 -4.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.646 r_dihedral_angle_3_deg 23.129 r_dihedral_angle_4_deg 20.633 r_dihedral_angle_1_deg 6.856 r_mcangle_it 1.853 r_scangle_it 1.837 r_angle_refined_deg 1.728 r_scbond_it 1.103 r_mcbond_it 1.074 r_nbtor_refined 0.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.646 r_dihedral_angle_3_deg 23.129 r_dihedral_angle_4_deg 20.633 r_dihedral_angle_1_deg 6.856 r_mcangle_it 1.853 r_scangle_it 1.837 r_angle_refined_deg 1.728 r_scbond_it 1.103 r_mcbond_it 1.074 r_nbtor_refined 0.354 r_symmetry_vdw_refined 0.307 r_symmetry_hbond_refined 0.304 r_nbd_refined 0.3 r_xyhbond_nbd_refined 0.215 r_xyhbond_nbd_other 0.137 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4501 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 42
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection