3CO3 | pdb_00003co3

X-Ray Crystal Structure of a Monofunctional Platinum-DNA Adduct, cis-{Pt(NH3)2(pyridine)}2+ Bound to Deoxyguanosine in a Dodecamer Duplex

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
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

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.44	α = 90
b = 66.01	β = 90
c = 56.05	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2007-04-04	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2007-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.072	APS	24-ID-C
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.984	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1,2	2.17	50	96	0.107	18.1	6.9	4836	4765

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.17	2.25	76		0.556		6.8	367

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.16	28.44	2	4836	4614	216	95.41	0.248	0.227	0.225	0.23	0.254	0.25	RANDOM	42.444

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]
0.09			0.04		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	7.387
r_mcbond_it	6.168
r_scbond_it	5.863
r_angle_refined_deg	1.435
r_nbtor_refined	0.349
r_symmetry_hbond_refined	0.218
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.142
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	7.387
r_mcbond_it	6.168
r_scbond_it	5.863
r_angle_refined_deg	1.435
r_nbtor_refined	0.349
r_symmetry_hbond_refined	0.218
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.142
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.089
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	486
Solvent Atoms	16
Heterogen Atoms	9

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.