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PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTRATE, INCORPORATED (-)3TC-MP AND AN ANOTHER INCOMING (-)3TC-TP NUCLEOTIDE.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 50 MM IMIDAZOLE, 350 MM SODIUM
ACETATE, 17% PEG3350 , PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.38 48.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.33 α = 90 b = 79.53 β = 107.39 c = 55.33 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 193 CCD RAYONIX MX225HE 2014-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
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 1.85 32.76 98.9 0.088 8.4 3.8 38657
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 1.85 1.89 98.7 0.686 2 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4RQ7 1.85 32.76 36763 1883 98.8 0.231 0.228 0.2276 0.279 0.2784 RANDOM 32.22
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] 0.36 0.21 0.08 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.87 r_dihedral_angle_3_deg 14.665 r_dihedral_angle_4_deg 12.188 r_dihedral_angle_1_deg 5.035 r_long_range_B_refined 4.973 r_long_range_B_other 4.829 r_scangle_other 2.833 r_mcangle_it 2.7 r_mcangle_other 2.699 r_scbond_it 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.87 r_dihedral_angle_3_deg 14.665 r_dihedral_angle_4_deg 12.188 r_dihedral_angle_1_deg 5.035 r_long_range_B_refined 4.973 r_long_range_B_other 4.829 r_scangle_other 2.833 r_mcangle_it 2.7 r_mcangle_other 2.699 r_scbond_it 1.73 r_scbond_other 1.73 r_mcbond_other 1.576 r_mcbond_it 1.575 r_angle_refined_deg 1.162 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.001 r_bond_other_d r_angle_other_deg 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 2354 Nucleic Acid Atoms 632 Solvent Atoms 252 Heterogen Atoms 52
Software Software Software Name Purpose MOSFLM data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement