9ICL

DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF PYROPHOSPHATE AND MNCL2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9ICK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR PYROPHOSPHATE (PPI), 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSIONS FOR THIS STRUCTURE.
Crystal Properties
Matthews coefficientSolvent content
359.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.634α = 90
b = 57.763β = 90
c = 48.491γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORSDMS1995-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.820916211843
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.88720.71.4

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONDIFFERENCE FOURIER9ICK2.82011843910.163
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]
RMS Deviations
KeyRefinement Restraint Deviation
t_dihedral_angle_d18.3
t_it5.7
t_angle_deg2.7
t_nbd0.024
t_bond_d0.019
t_trig_c_planes0.013
t_gen_planes0.005
t_incorr_chiral_ct
t_pseud_angle
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2623
Nucleic Acid Atoms248
Solvent Atoms152
Heterogen Atoms4

Software

Software
Software NamePurpose
TNTrefinement
SDMSdata reduction
SDMSdata scaling
TNTphasing