4NLN

Structure of human DNA polymerase beta complexed with nicked DNA containing a template 8BrG and incoming CTP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.514-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.4149.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.955α = 90
b = 79.075β = 106.59
c = 54.912γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.97648ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.26152.66799.6211692082211
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.261

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.26152.66719968102294.310.21370.21040.2732RANDOM38.0607
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]
0.611.81-0.430.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.113
r_dihedral_angle_4_deg17.671
r_dihedral_angle_3_deg16.76
r_dihedral_angle_1_deg6.14
r_angle_refined_deg1.842
r_chiral_restr0.108
r_bond_refined_d0.013
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2565
Nucleic Acid Atoms652
Solvent Atoms61
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing