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Single stranded DNA-binding protein (ICP8) from Herpes simplex virus-1, apo form. Mutations: C254S, C455S, K769A, E770A
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 7.5 293 2% PEG 8,000,
50mM HEPES, pH 7.5,
40mM MgCl2,
2mM DTT,
1mM Spermine
Crystal Properties Matthews coefficient Solvent content 2.38 48.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.99 α = 90 b = 140.2 β = 111.06 c = 98.8 γ = 90
Symmetry Space Group P 1 21 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 9M 2023-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920085 NSLS-II 17-ID-1
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 2.75 92.2 100 0.238 0.983 7.5 6.9 59439
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.85 1.03 0.735 2.5
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 (All) 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 2.75 92.2 59411 2968 99.988 0.188 0.1837 0.189 0.263 0.2637 RANDOM 36.627
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] 1.875 -0.146 -0.631 -0.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.156 r_dihedral_angle_6_deg 14.751 r_dihedral_angle_2_deg 13.343 r_lrange_it 8.718 r_lrange_other 8.718 r_dihedral_angle_1_deg 6.776 r_scangle_it 5.13 r_scangle_other 5.13 r_mcangle_it 4.695 r_mcangle_other 4.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.156 r_dihedral_angle_6_deg 14.751 r_dihedral_angle_2_deg 13.343 r_lrange_it 8.718 r_lrange_other 8.718 r_dihedral_angle_1_deg 6.776 r_scangle_it 5.13 r_scangle_other 5.13 r_mcangle_it 4.695 r_mcangle_other 4.694 r_scbond_it 3.175 r_scbond_other 3.175 r_mcbond_it 2.901 r_mcbond_other 2.901 r_angle_refined_deg 1.614 r_angle_other_deg 0.532 r_symmetry_nbd_refined 0.239 r_nbd_refined 0.22 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.184 r_nbd_other 0.165 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.07 r_symmetry_xyhbond_nbd_other 0.07 r_chiral_restr_other 0.011 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16092 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling PHASER phasing