2HTT | pdb_00002htt

Ruthenium Hexammine ion interactions with Z-DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XAMNDB ENTRY ZD0014

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.9293MPD, sodium cacodylate, ruthenium hexammine chloride, spermine, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.7294651.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.895α = 90
b = 35.895β = 90
c = 44.604γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMARRESEARCH2005-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
12.631.16930.08734.52.4312071207
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)
2.62.6994.80.2631.62.45181

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTNDB ENTRY ZD00142.6159899028796.490.2950.266650.25790.30.363710.34RANDOM9.391
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]
0.140.070.14-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg2.141
r_scangle_it1.885
r_scbond_it1.075
r_symmetry_vdw_refined0.307
r_nbtor_refined0.296
r_nbd_refined0.213
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.201
r_chiral_restr0.075
r_bond_refined_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms324
Solvent Atoms12
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
AUTOMARdata reduction
AMoREphasing