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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 6 0.1M NA-CACODYLATE PH 6.0, 100MM NACL, 100UM ZNAC2, 20% PEG 4K
Crystal Properties Matthews coefficient Solvent content 3.8 67.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.252 α = 90 b = 106.193 β = 90 c = 130.315 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 ADSC CCD 2004-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D APS 14-BM-D
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 2.1 81.65 92.5 0.06 14.4 4.3 55770 2
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 2.1 2.18 78.1 0.42 2.8 3.9
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 2.11 81.65 52889 2816 92.4 0.197 0.194 0.2002 0.247 0.2465 RANDOM 40.85
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] 3.85 0.96 -4.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.681 r_scangle_it 3.166 r_scbond_it 1.812 r_angle_refined_deg 1.523 r_mcangle_it 1.484 r_angle_other_deg 1.059 r_mcbond_it 0.794 r_symmetry_vdw_other 0.276 r_symmetry_hbond_refined 0.242 r_nbd_other 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.681 r_scangle_it 3.166 r_scbond_it 1.812 r_angle_refined_deg 1.523 r_mcangle_it 1.484 r_angle_other_deg 1.059 r_mcbond_it 0.794 r_symmetry_vdw_other 0.276 r_symmetry_hbond_refined 0.242 r_nbd_other 0.237 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.087 r_nbtor_other 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 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 4282 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing