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9YD2

Ternary complex of DNA polymerase I from Bacillus stearothermophilus, large fragment, bound to DNA containing a thymine dimer and dATP

Experimental procedure
Experimental methodSINGLE WAVELENGTH
Source typeSYNCHROTRON
Source detailsAPS BEAMLINE 22-BM
Synchrotron siteAPS
Beamline22-BM
Temperature [K]100
Detector technologyCCD
Collection date2015-03-26
DetectorMARMOSAIC 225 mm CCD
Wavelength(s)1.000
Spacegroup nameP 31 2 1
Unit cell lengths92.140, 92.140, 189.690
Unit cell angles90.00, 90.00, 120.00
Refinement procedure
Resolution79.796 - 2.249
Rwork0.225
R-free0.28530
Structure solution methodMOLECULAR REPLACEMENT
RMSD bond length0.009
RMSD bond angle1.948
Data reduction softwareXDS
Data scaling softwareXSCALE
Phasing softwarePHASER (2.8.3)
Refinement softwareREFMAC (5.8.0430)
Data quality characteristics
 OverallOuter shell
Low resolution limit [Å]79.8002.310
High resolution limit [Å]2.2492.249
Rmeas0.0631.000
Number of reflections447633028
<I/σ(I)>21.641.42
Completeness [%]99.392.4
Redundancy6.94.6
CC(1/2)0.9990.616
Crystallization Conditions
crystal IDmethodpHtemperaturedetails
1VAPOR DIFFUSION, HANGING DROP29046% (v/v) saturated ammonium sulfate, 10 mM manganese sulfate (MnSO4), 100 mM 2-(N-morpholino)ethanesulfonic acid (MES), 5% 2-methyl-1,3-propanediol (MPD), 1 mM 2',3'-dideoxyguanosine triphosphate, 5 mM 2'-deoxyadenosine triphosphate

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PDB entries from 2026-07-01

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