1BPY

HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5PROTEIN-DNA COMPLEX WAS CRYSTALLIZED USING A RESERVOIR CONTAINING 16.0% PEG 3350, 180 MM SODIUM ACETATE, AND 50 MM HEPES, PH 7.5., VAPOR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
2.141.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.543α = 90
b = 79.817β = 107.11
c = 54.942γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS1996-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-1SSRLBL7-1

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
12.220950.0862.621036
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)
12.22.2884.80.18

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 9ICW2.2202103621036207995.40.2270.2320.33
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_d22.1
t_it6.5
t_angle_deg3
t_bond_d0.02
t_nbd0.016
t_trig_c_planes0.015
t_gen_planes0.006
t_incorr_chiral_ct
t_pseud_angle
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2614
Nucleic Acid Atoms631
Solvent Atoms321
Heterogen Atoms31

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
TNTrefinement