4NLZ

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


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
2.4148.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.414α = 90
b = 79.438β = 105.37
c = 54.798γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.68352.83999.6126921258411
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.683

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 REPLACEMENTTHROUGHOUT2.68352.8391202159594.680.20430.19990.2906RANDOM22.2309
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]
0.810.34-0.33-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.68
r_dihedral_angle_3_deg18.983
r_dihedral_angle_4_deg16.453
r_dihedral_angle_1_deg5.865
r_angle_refined_deg1.664
r_chiral_restr0.098
r_bond_refined_d0.01
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2561
Nucleic Acid Atoms655
Solvent Atoms57
Heterogen Atoms8

Software

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