1IHH | pdb_00001ihh

2.4 ANGSTROM CRYSTAL STRUCTURE OF AN OXALIPLATIN 1,2-D(GPG) INTRASTRAND CROSS-LINK IN A DNA DODECAMER DUPLEX

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	MPD, SODIUM CACODYLATE, SPERMINE*4HCl, BACL2, ETHYL ACETATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.82	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.942	α = 90
b = 51.246	β = 90
c = 87.049	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	IMAGE PLATE	MARRESEARCH		2000-02-27	M	SINGLE WAVELENGTH
2	1	x-ray	173	CCD	CUSTOM-MADE		2000-02-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.970	SSRL	BL9-1
2	SYNCHROTRON	APS BEAMLINE 19-ID	1.0721,1.0724,1.0277,1.1206	APS	19-ID

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	2.4	100	93.7	0.089	18.9	9.76	61465	6296	4

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)
	2.4	2.44	69		0.368	4.5

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	FREE R	2.4	100	4	6296	4935	487	93.7	0.209	0.22	0.256	RANDOM	47.9

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
		508

RMS Deviations
Key	Refinement Restraint Deviation
s_similar_dist	0.106
s_angle_d	0.021
s_bond_d	0.007
s_non_zero_chiral_vol	0.006
s_from_restr_planes	0.001
s_zero_chiral_vol

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	486
Solvent Atoms	12
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SHELXL-97	refinement
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

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.