1M6F

Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DBEDNA PART OF NDB ENTRY GDL009

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5285MGCL2 2UL OF 75MM, DNA DOUBLE-STRANDED 3UL OF 2MM, MPD 2UL OF 25%, DRUG 2UL OF 4.5MM, SODIUM CACODYLATE 40MM. MPD IN RESERVOIR 700UL OF 50%., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.0640.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 24.098α = 90
b = 39.821β = 90
c = 65.62γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray104IMAGE PLATERIGAKU RAXIS IVYale Focussing Mirrors2002-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.781792.80.0478.8604011
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)
1.781.8490.690.60.184

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTDNA PART OF NDB ENTRY GDL0091.781024563654772980.2050.2020.277RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
s_angle_d0.02
s_from_restr_planes0.019
s_anti_bump_dis_restr0.01
s_bond_d0.008
s_non_zero_chiral_vol0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms486
Solvent Atoms111
Heterogen Atoms42

Software

Software
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing