1RGT

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JY1PDB structure 1JY1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8298PEG 3000, NaCl, HEPES, spermine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2645.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.791α = 90
b = 104.894β = 90
c = 194.124γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.9791ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125097.40.08515.294.1568032-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0791.20.3683.38

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-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUTPDB structure 1JY12506798164557342497.460.195950.195950.194280.22761RANDOM23.713
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]
-1.42.7-1.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.157
r_scangle_it3.745
r_scbond_it2.481
r_mcangle_it2.382
r_mcbond_it1.457
r_angle_refined_deg1.161
r_angle_other_deg0.762
r_nbd_other0.437
r_symmetry_vdw_refined0.245
r_nbd_refined0.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.157
r_scangle_it3.745
r_scbond_it2.481
r_mcangle_it2.382
r_mcbond_it1.457
r_angle_refined_deg1.161
r_angle_other_deg0.762
r_nbd_other0.437
r_symmetry_vdw_refined0.245
r_nbd_refined0.209
r_nbtor_other0.192
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.176
r_metal_ion_refined0.109
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6827
Nucleic Acid Atoms100
Solvent Atoms222
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing