9ICM

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DOUBLE STRANDED DNA (NO 5'-PHOSPHATE)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5THIS ENTRY DESCRIBES THE SAME CRYSTAL STRUCTURE REPORTED IN ENTRY 9ICW, WITH THE EXCEPTION THAT THE DNA STRAND DESIGNATED AS THE PRIMER IS NOT 5'-PHOSPHORYLATED. SEE REFERENCE 1 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSIONS FOR THIS STRUCTURE., pH 6.50
Crystal Properties
Matthews coefficientSolvent content
359.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.698α = 90
b = 57.867β = 90
c = 48.556γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORSDMS1995-04-09MSINGLE 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
12.920890.0481.810507
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)
2.93820.1511.5

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 FOURIER9ICW2.92010507890.155
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_d18.4
t_angle_deg2.8
t_nbd0.026
t_bond_d0.018
t_trig_c_planes0.014
t_gen_planes0.005
t_incorr_chiral_ct
t_pseud_angle
t_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2623
Nucleic Acid Atoms248
Solvent Atoms154
Heterogen Atoms2

Software

Software
Software NamePurpose
SDMSdata collection
SDMSdata reduction
TNTrefinement
SDMSdata scaling
TNTphasing