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The crystal structure of dGTPalphaSe-Rp: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 0.2 M L-proline, HEPES pH 8.6 (0.1 M),10% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.8 56.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.481 α = 90 b = 77.382 β = 90 c = 111.353 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 2016-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
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 3 30 99.9 0.117 7.8 12.7 10889
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 3 29.74 9335 515 91.5 0.22365 0.22045 0.259 0.28371 0.3164 RANDOM 34.522
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] -23.49 -0.12 23.61
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 70.625 r_dihedral_angle_2_deg 32.83 r_dihedral_angle_4_deg 16.686 r_dihedral_angle_3_deg 16.056 r_sphericity_bonded 12.954 r_dihedral_angle_1_deg 6.086 r_long_range_B_refined 6.033 r_long_range_B_other 6.017 r_mcangle_it 4.589 r_mcangle_other 4.587
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 70.625 r_dihedral_angle_2_deg 32.83 r_dihedral_angle_4_deg 16.686 r_dihedral_angle_3_deg 16.056 r_sphericity_bonded 12.954 r_dihedral_angle_1_deg 6.086 r_long_range_B_refined 6.033 r_long_range_B_other 6.017 r_mcangle_it 4.589 r_mcangle_other 4.587 r_scangle_other 4.459 r_scbond_it 3.33 r_scbond_other 3.329 r_mcbond_it 3.251 r_mcbond_other 3.251 r_rigid_bond_restr 3.058 r_angle_refined_deg 1.416 r_angle_other_deg 1.076 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2650 Nucleic Acid Atoms 358 Solvent Atoms 4 Heterogen Atoms 66
Software Software Software Name Purpose HKL-3000 data reduction HKL-3000 data scaling PHASER phasing REFMAC refinement