1G3X

INTERCALATION OF AN 9ACRIDINE-PEPTIDE DRUG IN A DNA DODECAMER


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.5 mM duplex, 1mM drug-peptide adduct, 20 mM NaCacodylate, 100 mM MgCl2, 45% MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8834.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.471α = 90
b = 68.365β = 90
c = 77.362γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH1998-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HamburgX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.73091.20.05413.38.812155
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.73.290.30.2231.64

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.720808692189.050.224760.220050.26607RANDOM37.54
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]
-4.66-1.215.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg31.341
r_dihedral_angle_1_deg3.978
r_angle_refined_deg2.409
r_scangle_it1.875
r_scbond_it1.37
r_mcangle_it1.136
r_mcbond_it0.457
r_symmetry_hbond_refined0.152
r_nbd_refined0.129
r_xyhbond_nbd_refined0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg31.341
r_dihedral_angle_1_deg3.978
r_angle_refined_deg2.409
r_scangle_it1.875
r_scbond_it1.37
r_mcangle_it1.136
r_mcbond_it0.457
r_symmetry_hbond_refined0.152
r_nbd_refined0.129
r_xyhbond_nbd_refined0.128
r_symmetry_vdw_refined0.119
r_chiral_restr0.099
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms48
Nucleic Acid Atoms2897
Solvent Atoms61
Heterogen Atoms49

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling