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The crystal structure of native dGTP:DNApre-I: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 acetate (0.2 M), BIS-Tris pH=5.5 (0.1 M), 20% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.59 52.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.706 α = 90 b = 75.441 β = 90 c = 108.45 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 2018-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 30 93.5 0.814 26.6 5.1 21028
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 0.256
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 2.25 28.52 21028 1128 94.18 0.21494 0.21216 0.2062 0.26325 0.271 RANDOM 49.861
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] 6.97 -5.53 -1.44
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 74.507 r_dihedral_angle_2_deg 30.797 r_dihedral_angle_4_deg 16.005 r_dihedral_angle_3_deg 14.202 r_sphericity_bonded 10.191 r_dihedral_angle_1_deg 5.175 r_rigid_bond_restr 1.709 r_angle_refined_deg 1.164 r_angle_other_deg 1.064 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 74.507 r_dihedral_angle_2_deg 30.797 r_dihedral_angle_4_deg 16.005 r_dihedral_angle_3_deg 14.202 r_sphericity_bonded 10.191 r_dihedral_angle_1_deg 5.175 r_rigid_bond_restr 1.709 r_angle_refined_deg 1.164 r_angle_other_deg 1.064 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2763 Nucleic Acid Atoms 358 Solvent Atoms 75 Heterogen Atoms 74
Software Software Software Name Purpose HKL-3000 data scaling HKL-3000 data reduction PHASER phasing REFMAC refinement