3GGK

Locating monovalent cations in one turn of G/C rich B-DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	MPD, Magnesium acetate, Rubidium acetate, Rubidium hydroxide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.135	α = 90
b = 25.156	β = 116.24
c = 34.113	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	MARMOSAIC 300 mm CCD		2004-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.81528	APS	22-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	0.784	30.6	63.9	0.074	23	6.2		19281

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	DNA coordinates from PDB Entry 1bd1 (Heinemann and Alings)	0.87	30.6	17543	17543	1047	90.55	0.11971	0.1188	0.1343	RANDOM	7.764

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]
0.2		-0.14	-0.14		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	3.647
r_sphericity_free	3.401
r_angle_refined_deg	1.833
r_scangle_it	1.633
r_scbond_it	1.339
r_rigid_bond_restr	0.839
r_nbtor_refined	0.302
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.16
r_symmetry_hbond_refined	0.114
r_chiral_restr	0.104
r_xyhbond_nbd_refined	0.099
r_gen_planes_refined	0.025
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	287
Solvent Atoms	156
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing