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Herpes simplex virus glycoprotein D bound to the human receptor nectin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C36 2C36, 1NEU AND 3ALP experimental model PDB 1NEU 2C36, 1NEU AND 3ALP experimental model PDB 3ALP 2C36, 1NEU AND 3ALP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.2 293 1.0 M Na2HPO4/KH2PO4 pH 7.2 and 300 mM NH4SO4, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.66 73.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.003 α = 90 b = 188.003 β = 90 c = 185.004 γ = 120
Symmetry Space Group P 32 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 2005-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 4 49.1 99.9 0.06 8 2.6 31947 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4 4.1 99.2 0.208 1.7 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2C36, 1NEU AND 3ALP 4 30 30529 30227 1675 98.9 0.267 0.266 0.2607 0.287 0.2749 RANDOM 151.77
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] 144.41 144.41 -288.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.219 r_dihedral_angle_3_deg 21.664 r_scangle_it 20.5 r_dihedral_angle_4_deg 19.243 r_scbond_it 14.485 r_dihedral_angle_1_deg 8.905 r_mcangle_it 8.412 r_mcbond_it 5.527 r_angle_refined_deg 1.747 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.219 r_dihedral_angle_3_deg 21.664 r_scangle_it 20.5 r_dihedral_angle_4_deg 19.243 r_scbond_it 14.485 r_dihedral_angle_1_deg 8.905 r_mcangle_it 8.412 r_mcbond_it 5.527 r_angle_refined_deg 1.747 r_chiral_restr 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d r_angle_other_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 9592 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 310
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling