1KFV

Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EE8PDB ENTRY 1EE8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.7293PEG4K, LiSO4, TCEP, Tris-HCl, spermidine, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1643.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.88α = 90
b = 62.03β = 104.7
c = 80.97γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrors2001-06-20MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9788ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.542598.70.0870.0536.13.1221852189755
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.542.6794.30.2880.2091.42.3

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 DIFFRACTIONMolecular replacement combined with MADfree RPDB ENTRY 1EE82.55252206221858216699.10.2510.285random40
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
x_angle_deg1.3
x_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4210
Nucleic Acid Atoms1026
Solvent Atoms54
Heterogen Atoms14

Software

Software
Software NamePurpose
SnBphasing
SOLVEphasing
MOLREPphasing
CNSrefinement
DENZOdata reduction
CCP4data scaling