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Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 18% PEG3350
0.3M NaH2PO4
0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.584 α = 90 b = 92.6 β = 90 c = 130.235 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 ADSC QUANTUM 315 monochromator Si(111) 2006-03-31 M SINGLE WAVELENGTH 2 1 3 1 4 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.115870 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 21.134 87 0.07 0.07 9.1 5.2 48388 1.1 1.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 69.5 0.724 0.724 1.1 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 2.3 20 40374 38353 2021 89.75 0.18984 0.18623 0.1845 0.25811 0.2531 RANDOM 41.619
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] -2.28 3.28 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.581 r_dihedral_angle_3_deg 20.138 r_dihedral_angle_4_deg 19.806 r_dihedral_angle_1_deg 6.361 r_scangle_it 2.443 r_scbond_it 1.601 r_angle_refined_deg 1.551 r_mcangle_it 0.954 r_mcbond_it 0.587 r_symmetry_hbond_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.581 r_dihedral_angle_3_deg 20.138 r_dihedral_angle_4_deg 19.806 r_dihedral_angle_1_deg 6.361 r_scangle_it 2.443 r_scbond_it 1.601 r_angle_refined_deg 1.551 r_mcangle_it 0.954 r_mcbond_it 0.587 r_symmetry_hbond_refined 0.332 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 7147 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 15
Software Software Software Name Purpose SCALA data scaling SHELX phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SHELXD phasing