1ZQZ

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (50 MILLIMOLAR)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZQU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% TRIS-HCL, 100 MILLIMOLAR, PH 7.5 MNCL2, 50 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.565α = 90
b = 62.728β = 90
c = 37.458γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298AREA DETECTORXUONG-HAMLIN MULTIWIRE1996-01-10M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R

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
12.720950.0798.92.97763
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)
2.72.8840.2112.11.8

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONDIFFERENCE FOURIER1ZQU2.720776395
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_d22.2
t_it6.2
t_angle_deg2.9
t_nbd0.033
t_bond_d0.021
t_trig_c_planes0.019
t_gen_planes0.008
t_incorr_chiral_ct
t_pseud_angle
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1935
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms2

Software

Software
Software NamePurpose
TNTrefinement
SDMSdata reduction
SDMSdata scaling
TNTphasing