1K3W

Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherinitial MODEL OF BR-URACIL-CONTAINING DNA COMPLEXED WITH ENDONUCLEASE VIII AT 2.4A RESOLUTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52881.8M Ammonium-sulfate, 0.1M sodium-citrate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
3.0360.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.03α = 90
b = 76.03β = 90
c = 164.933γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26CNSLSX26C

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
11.424095.20.0838.95.586586
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)
1.421.4471.40.37523191

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFREE Rinitial MODEL OF BR-URACIL-CONTAINING DNA COMPLEXED WITH ENDONUCLEASE VIII AT 2.4A RESOLUTION1.42107610876108852195.20.16460.2026RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
3382830.41
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.092
s_non_zero_chiral_vol0.07
s_zero_chiral_vol0.06
s_similar_adp_cmpnt0.039
s_angle_d0.035
s_from_restr_planes0.0255
s_anti_bump_dis_restr0.022
s_bond_d0.014
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2080
Nucleic Acid Atoms381
Solvent Atoms397
Heterogen Atoms16

Software

Software
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing