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The crystal structure of dGTPalphaSe-Sp:DNApre-II:Pol X substrate ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HRB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 ammonium sulfate (0.2 M), Bis-Tris pH 5.5 (0.1 M), 20% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.666 α = 90 b = 78.19 β = 90 c = 101.304 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 MARMOSAIC 325 mm CCD 2016-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.977 SSRF BL17U1
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 2.3 30 99.9 0.117 7.8 12.7 21788
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 3 3.11 100 1.225 12.8
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 2.3 30 20337 1096 98.89 0.20647 0.20437 0.2095 0.24462 0.2488 RANDOM 31.343
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] -0.15 -0.44 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_dihedral_angle_4_deg 16.993 r_dihedral_angle_3_deg 14.507 r_dihedral_angle_1_deg 5.609 r_long_range_B_refined 4.43 r_long_range_B_other 4.43 r_scangle_other 2.899 r_mcangle_it 2.722 r_mcangle_other 2.721 r_scbond_it 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_dihedral_angle_4_deg 16.993 r_dihedral_angle_3_deg 14.507 r_dihedral_angle_1_deg 5.609 r_long_range_B_refined 4.43 r_long_range_B_other 4.43 r_scangle_other 2.899 r_mcangle_it 2.722 r_mcangle_other 2.721 r_scbond_it 1.72 r_scbond_other 1.72 r_mcbond_it 1.607 r_mcbond_other 1.605 r_angle_refined_deg 1.385 r_angle_other_deg 1.014 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 2840 Nucleic Acid Atoms 717 Solvent Atoms 70 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing