1RFF

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JY1PDB entry 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
2.2344.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.076α = 90
b = 104.904β = 90
c = 193.832γ = 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 8.2.21.00ALS8.2.2

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
11.75090.60.07121.044.52103225103255-3
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)
1.71.7664.60.4822

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 1jy11.75010283397672516190.780.193640.193640.192580.21325RANDOM24.569
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]
-0.632-1.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.254
r_scangle_it4.29
r_scbond_it2.824
r_mcangle_it2.754
r_mcbond_it1.745
r_angle_refined_deg1.335
r_symmetry_vdw_refined0.211
r_nbd_refined0.205
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.254
r_scangle_it4.29
r_scbond_it2.824
r_mcangle_it2.754
r_mcbond_it1.745
r_angle_refined_deg1.335
r_symmetry_vdw_refined0.211
r_nbd_refined0.205
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.156
r_chiral_restr0.102
r_metal_ion_refined0.1
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6933
Nucleic Acid Atoms102
Solvent Atoms343
Heterogen Atoms34

Software

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