2RBA

Structure of Human Thymine DNA Glycosylase Bound to Abasic and Undamaged DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WYWPDB ENTRY 1wyw, SUMO removed

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52958 mg/ml protein and 20% molar excess DNA duplex in 10mM Tris-HCL, 100 mM NaCl, 0.5mM DTT. Reservoir: 20% PEG 3350, 0.2M K/Na tartrate tetrahydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.5465.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 162.133α = 90
b = 162.133β = 90
c = 56.142γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105CCDADSC QUANTUM 3152007-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.91837SSRLBL9-1

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
12.795099.60.0830.08325.510.4211372113787.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.792.8996.817.92031

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 1wyw, SUMO removed2.795019458104897.490.232110.229650.27629RANDOM110.074
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]
-4.52-2.26-4.526.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.864
r_dihedral_angle_4_deg24.614
r_dihedral_angle_3_deg22.542
r_dihedral_angle_1_deg9.62
r_scangle_it2.984
r_angle_refined_deg2.272
r_scbond_it1.839
r_mcangle_it1.66
r_mcbond_it0.978
r_nbtor_refined0.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.864
r_dihedral_angle_4_deg24.614
r_dihedral_angle_3_deg22.542
r_dihedral_angle_1_deg9.62
r_scangle_it2.984
r_angle_refined_deg2.272
r_scbond_it1.839
r_mcangle_it1.66
r_mcbond_it0.978
r_nbtor_refined0.338
r_nbd_refined0.29
r_symmetry_vdw_refined0.289
r_symmetry_hbond_refined0.246
r_xyhbond_nbd_refined0.208
r_chiral_restr0.17
r_bond_refined_d0.02
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2916
Nucleic Acid Atoms929
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing