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Poly dA 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 7.5 293 0.02 M magnesium chloride, 0.05 M PIPES, pH 7.5, 4% PEG8000, 0.001 M spermine
Crystal Properties Matthews coefficient Solvent content 4.12 70.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.171 α = 90 b = 151.171 β = 90 c = 154.561 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 0.979330 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 3 154.56 100 0.053 0.998 11.7 1.9 41340
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 3 3.12 100 0.828 0.312 1
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 3 130.918 41302 2119 99.978 0.202 0.1997 0.2055 0.2377 0.2546 RANDOM 37.108
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] -3.536 -1.768 -3.536 11.469
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.444 r_dihedral_angle_6_deg 14.169 r_lrange_it 9.147 r_lrange_other 9.147 r_dihedral_angle_1_deg 8.262 r_scangle_it 5.026 r_scangle_other 5.025 r_mcangle_it 4.524 r_mcangle_other 4.523 r_scbond_it 2.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.444 r_dihedral_angle_6_deg 14.169 r_lrange_it 9.147 r_lrange_other 9.147 r_dihedral_angle_1_deg 8.262 r_scangle_it 5.026 r_scangle_other 5.025 r_mcangle_it 4.524 r_mcangle_other 4.523 r_scbond_it 2.995 r_scbond_other 2.994 r_mcbond_it 2.678 r_mcbond_other 2.678 r_angle_refined_deg 1.353 r_angle_other_deg 0.462 r_nbd_refined 0.246 r_nbd_other 0.202 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_nbd_refined 0.129 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.072 r_chiral_restr 0.059 r_dihedral_angle_other_2_deg 0.026 r_ext_dist_refined_b 0.024 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8052 Nucleic Acid Atoms 168 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB-REDO refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing