4M2Y

Structure of human DNA polymerase beta complexed with 8-BrG as the template base in a 1-nucleotide gapped DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ISBPDB ENTRY 3ISB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529514-23% PEG 3340, 350mM sodium acetate in 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4549.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.554α = 90
b = 79.271β = 105.48
c = 54.915γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-03-06MSINGLE 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
12.272097.12022820228

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 3ISB2.2719.8319695101194.270.21510.2120.2694RANDOM28.3099
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]
0.810.44-0.49-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.116
r_dihedral_angle_3_deg16.947
r_dihedral_angle_4_deg16.637
r_dihedral_angle_1_deg5.83
r_mcangle_it2.731
r_mcbond_it1.756
r_mcbond_other1.745
r_angle_refined_deg1.651
r_angle_other_deg1.148
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.116
r_dihedral_angle_3_deg16.947
r_dihedral_angle_4_deg16.637
r_dihedral_angle_1_deg5.83
r_mcangle_it2.731
r_mcbond_it1.756
r_mcbond_other1.745
r_angle_refined_deg1.651
r_angle_other_deg1.148
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2543
Nucleic Acid Atoms633
Solvent Atoms72
Heterogen Atoms2

Software

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