3EY0

A new form of DNA-drug interaction in the minor groove of a coiled coil


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOtherstandard watson-crick DNA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6278.1520 mM MgCl2, 50 mM MES, 15% Isopropanol, 3.62 mM ds-DNA, 16.86 mM PNT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278.15K
Crystal Properties
Matthews coefficientSolvent content
2.8656.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 27.789α = 90
b = 27.789β = 90
c = 311.95γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray104CCDADSC QUANTUM 210Mirrors2008-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM160.97950ESRFBM16

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.525094.70.0980.09837.62515.828992899-356.01
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.522.561000.2120.21215.7518.4128

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTstandard watson-crick DNA2.52502782251126293.620.221930.215720.27715RANDOM43.499
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]
0.220.110.22-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.644
r_scangle_it1.577
r_angle_other_deg1.224
r_scbond_it1.028
r_chiral_restr0.052
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms404
Solvent Atoms51
Heterogen Atoms26

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling