1RH0

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine and trinucleotide GTT


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
2.2745.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.692α = 90
b = 104.75β = 90
c = 194.033γ = 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
12.35099.10.11813.724.94640746407-3
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)
2.32.3650.50.5052.53

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 1JY12.3504564243330231299.120.190520.190520.188190.2347RANDOM27.645
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]
-1.192.59-1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.279
r_scangle_it4.053
r_scbond_it2.712
r_mcangle_it2.616
r_mcbond_it1.523
r_angle_refined_deg1.241
r_nbd_other0.428
r_nbtor_other0.237
r_nbd_refined0.216
r_symmetry_vdw_refined0.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.279
r_scangle_it4.053
r_scbond_it2.712
r_mcangle_it2.616
r_mcbond_it1.523
r_angle_refined_deg1.241
r_nbd_other0.428
r_nbtor_other0.237
r_nbd_refined0.216
r_symmetry_vdw_refined0.208
r_xyhbond_nbd_refined0.186
r_angle_other_deg0.12
r_metal_ion_refined0.12
r_symmetry_hbond_refined0.102
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6820
Nucleic Acid Atoms80
Solvent Atoms227
Heterogen Atoms38

Software

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