3KHC

Crystal Structure of Escherichia coli AlkB in complex with ssDNA containing a 1-methylguanine lesion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FD8PDB ENTRY 2FD8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP628810-20% PEG 8000, 0.1M MES, 0.1M sodium chloride, 0.1M magnesium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.1542.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 147.809α = 90
b = 41.441β = 120.98
c = 85.622γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 922009-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
12.242.6999.60.1049.46.942290921726
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)
12.22.2399.940.3969.46.271661

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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 REPLACEMENTTHROUGHOUTPDB ENTRY 2FD82.223.7421726115699.680.214340.211260.27326RANDOM18.165
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]
-0.190.15-0.130.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.975
r_dihedral_angle_4_deg17.682
r_dihedral_angle_3_deg16.879
r_dihedral_angle_1_deg6.632
r_scangle_it1.998
r_angle_refined_deg1.619
r_scbond_it1.191
r_mcangle_it0.734
r_mcbond_it0.396
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.975
r_dihedral_angle_4_deg17.682
r_dihedral_angle_3_deg16.879
r_dihedral_angle_1_deg6.632
r_scangle_it1.998
r_angle_refined_deg1.619
r_scbond_it1.191
r_mcangle_it0.734
r_mcbond_it0.396
r_chiral_restr0.087
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3243
Nucleic Acid Atoms246
Solvent Atoms269
Heterogen Atoms22

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling