5IHD

Calcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), complexed by L-lactate and succinate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DCG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH62961.2 mM d(CG)3, 1.2 mM di copper complex, 0.25 M MES pH 6, 25 mM Ca(lactate)2, 2.5% EtOAc
Crystal Properties
Matthews coefficientSolvent content
238.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 27.487α = 90
b = 35.576β = 107.5
c = 31.044γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray183IMAGE PLATESTOE2005-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBELong fine focus1.54

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
11.5726.21597.90.06916.516.8793442
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)
11.571.7890.17363.772.96

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2DCG1.5726.2151.39793440897.90.1620.16050.19
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
f_dihedral_angle_d29.428
f_angle_d1.048
f_chiral_restr0.054
f_bond_d0.007
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms480
Solvent Atoms133
Heterogen Atoms26

Software

Software
Software NamePurpose
PHENIXrefinement
X-Areadata reduction
XSCALEdata scaling
SHELXSphasing