9ICW

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; NATIVE STRUCTURE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BPB1BPB, 2BPG
experimental modelPDB 2BPG1BPB, 2BPG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5SEE 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 = 178.638α = 90
b = 57.846β = 90
c = 48.489γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORSDMS1991-09-12M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.620950.0632.815291
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.7810.2022

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 DIFFRACTIONMOLECULAR REPLACEMENT1BPB, 2BPG2.62015291950.175
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_it6.1
t_angle_deg2.9
t_nbd0.025
t_bond_d0.021
t_trig_c_planes0.018
t_gen_planes0.006
t_incorr_chiral_ct
t_pseud_angle
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2623
Nucleic Acid Atoms248
Solvent Atoms157
Heterogen Atoms7

Software

Software
Software NamePurpose
X-PLORmodel building
TNTrefinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing