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Poly dT bound form of Single stranded DNA-binding protein(ICP8) from Herpes simplex virus-1. Mutations: C254S, C455S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1URJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M ammonium acetate, 0.02 M magnesium chloride, 0.05 M HEPES, pH 7.0, 5% PEG8000
Crystal Properties Matthews coefficient Solvent content 4.08 69.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.736 α = 90 b = 151.736 β = 90 c = 154.094 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 PIXEL DECTRIS EIGER X 16M 2022-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97933 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.1 77.06 100 0.118 0.998 7.1 16.6 37723
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.24 100 0.658 0.561 1.3 17.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.1 60.51 35714 1883 99.86 0.19501 0.19295 0.2034 0.23274 0.2349 RANDOM 77.973
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] 0.03 0.02 0.03 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.31 r_dihedral_angle_3_deg 20.438 r_long_range_B_refined 16.335 r_long_range_B_other 16.335 r_scangle_other 11.122 r_mcangle_it 9.703 r_mcangle_other 9.703 r_scbond_it 7.04 r_scbond_other 7.039 r_mcbond_other 6.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.31 r_dihedral_angle_3_deg 20.438 r_long_range_B_refined 16.335 r_long_range_B_other 16.335 r_scangle_other 11.122 r_mcangle_it 9.703 r_mcangle_other 9.703 r_scbond_it 7.04 r_scbond_other 7.039 r_mcbond_other 6.282 r_mcbond_it 6.281 r_dihedral_angle_1_deg 6.263 r_angle_refined_deg 1.518 r_angle_other_deg 0.516 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8202 Nucleic Acid Atoms 160 Solvent Atoms 4 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction XDS data reduction Aimless data scaling