3CO3
X-Ray Crystal Structure of a Monofunctional Platinum-DNA Adduct, cis-{Pt(NH3)2(pyridine)}2+ Bound to Deoxyguanosine in a Dodecamer Duplex
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-C |
Synchrotron site | APS |
Beamline | 24-ID-C |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2007-04-04 |
Detector | ADSC QUANTUM 315 |
Wavelength(s) | 1.072 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 46.440, 66.010, 56.050 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 28.440 - 2.160 |
R-factor | 0.227 |
Rwork | 0.225 |
R-free | 0.25400 |
Structure solution method | SAD |
RMSD bond length | 0.006 |
RMSD bond angle | 1.435 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | SHARP |
Refinement software | REFMAC |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.250 |
High resolution limit [Å] | 2.170 | 4.670 | 2.170 |
Rmerge | 0.107 | 0.106 | 0.556 |
Number of reflections | 4765 | ||
<I/σ(I)> | 18.1 | ||
Completeness [%] | 96.0 | 92.1 | 76 |
Redundancy | 6.9 | 6.3 | 6.8 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 120 mM Mg(acetate), 50 mM Na cacodylate, 1 mM spermine, 28% w/v PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 120 mM Mg(acetate), 50 mM Na cacodylate, 1 mM spermine, 28% w/v PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
Crystallization Reagents
ID | crystal ID | solution ID | reagent name | concentration | details |
1 | 1 | 1 | Mg(acetate) | ||
10 | 1 | 2 | H2O | ||
2 | 1 | 1 | Na cacodylate | ||
3 | 1 | 1 | spermine | ||
4 | 1 | 1 | PEG4000 | ||
5 | 1 | 1 | H2O | ||
6 | 1 | 2 | Mg(acetate) | ||
7 | 1 | 2 | Na cacodylate | ||
8 | 1 | 2 | spermine | ||
9 | 1 | 2 | PEG4000 |