1RG1

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RFFPDB entry 1RFF

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
2.2645.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.8α = 90
b = 104.711β = 90
c = 193.751γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-12-01MSINGLE 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
12.15094.20.10810.53.1956460-3
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)
2.12.1891.70.6011.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1RFF2.1505641053558285293.980.201440.201440.199440.23903RANDOM28.839
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]
-0.811.45-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.299
r_scangle_it3.846
r_scbond_it2.583
r_mcangle_it2.5
r_mcbond_it1.53
r_angle_refined_deg1.245
r_nbd_other0.42
r_nbtor_other0.333
r_symmetry_vdw_refined0.27
r_nbd_refined0.213
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.299
r_scangle_it3.846
r_scbond_it2.583
r_mcangle_it2.5
r_mcbond_it1.53
r_angle_refined_deg1.245
r_nbd_other0.42
r_nbtor_other0.333
r_symmetry_vdw_refined0.27
r_nbd_refined0.213
r_symmetry_hbond_refined0.208
r_xyhbond_nbd_refined0.196
r_angle_other_deg0.184
r_chiral_restr0.091
r_metal_ion_refined0.046
r_bond_refined_d0.011
r_bond_other_d0.006
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6818
Nucleic Acid Atoms102
Solvent Atoms198
Heterogen Atoms38

Software

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