6U16

Human thymine DNA glycosylase N140A mutant bound to DNA with 5-carboxyl-dC substrate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6295PEG 3350, Ammonium Acetate, Sodium Acetate
Crystal Properties
Matthews coefficientSolvent content
2.3748.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.57α = 90
b = 53.23β = 94.84
c = 81.32γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97946SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.681.0397.30.110.120.0470.9976.76.25172026.65
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6398.22.9883.2621.2870.2886.2

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 REPLACEMENTTHROUGHOUT5T2W1.642.31517102423970.1880.1860.21RANDOM44.36
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]
-5.84584.48321.12844.7174
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion22.65
t_omega_torsion3.43
t_angle_deg0.98
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion22.65
t_omega_torsion3.43
t_angle_deg0.98
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1540
Nucleic Acid Atoms1145
Solvent Atoms308
Heterogen Atoms12

Software

Software
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing