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Crystal structure of a DNA polymerase III alpha-epsilon chimera
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HNH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 279 0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.017 α = 90 b = 56.98 β = 93.78 c = 135.073 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 100 CCD ADSC QUANTUM 315r beamline optics 2012-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95369 Australian Synchrotron MX2
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 2.15 50 97.2 0.095 10.41 3.1 67257 67257 -1 -1
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 2.15 2.19 0.499 1.9 2.9 3361
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2HNH 2.15 35.28 67126 67126 3384 96.91 0.22948 0.22948 0.2262 0.2307 0.29079 0.2971 RANDOM 22.248
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] 2.45 1.09 0.63 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.85 r_dihedral_angle_4_deg 22.254 r_dihedral_angle_3_deg 17.169 r_scangle_it 7.272 r_dihedral_angle_1_deg 6.613 r_scbond_it 5.553 r_mcangle_it 3.475 r_mcbond_it 2.504 r_angle_refined_deg 1.745 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.85 r_dihedral_angle_4_deg 22.254 r_dihedral_angle_3_deg 17.169 r_scangle_it 7.272 r_dihedral_angle_1_deg 6.613 r_scbond_it 5.553 r_mcangle_it 3.475 r_mcbond_it 2.504 r_angle_refined_deg 1.745 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9700 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing