4M47

structure of human DNA polymerase complexed with 8-BrG in the template base paired with incoming non-hydrolyzable GTP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529514% - 23% PEG3400 and 350 mM sodium acetate in 50 mM imidazole , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4850.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.175α = 90
b = 79.267β = 107.8
c = 55.294γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-06-17MSINGLE 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
12.372096.41781317813

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.3719.82178131740589496.40.2120.20860.2725RANDOM41.9403
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]
-0.712.13-2.231.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.509
r_dihedral_angle_3_deg16.866
r_dihedral_angle_4_deg15.736
r_dihedral_angle_1_deg6.491
r_mcangle_it4.288
r_mcbond_it2.887
r_mcbond_other2.887
r_angle_refined_deg1.623
r_angle_other_deg1.157
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.509
r_dihedral_angle_3_deg16.866
r_dihedral_angle_4_deg15.736
r_dihedral_angle_1_deg6.491
r_mcangle_it4.288
r_mcbond_it2.887
r_mcbond_other2.887
r_angle_refined_deg1.623
r_angle_other_deg1.157
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2487
Nucleic Acid Atoms633
Solvent Atoms58
Heterogen Atoms35

Software

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