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Structure of unliganded HSV gD reveals a mechanism for receptor- mediated activation of virus entry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L2G PDB ENTRY 1L2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 100MM NA ACETATE PH 4.6, 10MM ZNCL2, 24% PEG &K
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.629 α = 90 b = 79.105 β = 90 c = 123.563 γ = 90
Symmetry Space Group P 21 21 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 CCD MARRESEARCH 2004-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 50 99.6 0.08 9 7.3 23602 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 98.2 0.34 5.07 7.1
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 1L2G 2.5 25 22271 1212 99.7 0.228 0.226 0.2222 0.275 0.2553 RANDOM 39
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] 1.37 0.6 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.806 r_scangle_it 3.412 r_scbond_it 2.011 r_angle_refined_deg 1.685 r_mcangle_it 1.655 r_angle_other_deg 0.931 r_mcbond_it 0.903 r_symmetry_vdw_refined 0.323 r_symmetry_vdw_other 0.243 r_nbd_other 0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.806 r_scangle_it 3.412 r_scbond_it 2.011 r_angle_refined_deg 1.685 r_mcangle_it 1.655 r_angle_other_deg 0.931 r_mcbond_it 0.903 r_symmetry_vdw_refined 0.323 r_symmetry_vdw_other 0.243 r_nbd_other 0.235 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.105 r_nbtor_other 0.09 r_bond_refined_d 0.017 r_symmetry_hbond_refined 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4067 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing