4KLH

DNA polymerase beta matched product complex with Mn2+, 40 s


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FMSPDB ENTRY 2FMS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829150 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2344.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.9α = 90
b = 80.2β = 107.9
c = 55.1γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 92mirrors2012-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
11.8765097.30.0750.07519.44.63482233530-3
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)
11.8761.9588.60.5160.5162.0392.8

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 2FMS1.87625.08930493304985.730.21090.20460.2694RANDOM32.6281
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]
3.02493.9536-0.2389-2.7859
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.287
f_angle_d1.114
f_chiral_restr0.064
f_bond_d0.012
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2614
Nucleic Acid Atoms651
Solvent Atoms264
Heterogen Atoms17

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
PHENIXphasing