5XEW | pdb_00005xew

Crystal structure of the [Ni2+-(chromomycin A3)2]-CCG repeats complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	1.0 mM single stranded-DNA, 2.0 mM Chromomycin A3, 4mM NiSO4 6H2O, 50 mM sodium-cacodylate buffer, 5 mM MgCl2, 1 mM spermine, 3 % MPD

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.291	α = 90
b = 48.291	β = 90
c = 83.356	γ = 120

Symmetry
Space Group	P 32 1 2

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 315r		2013-01-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.45104,1.48491,1.48582	NSRRC	BL13B1

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	1.75	30	99.6	0.05	28.2	10.1		21692			30.69

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)
1	1.75	1.81	96.5		0.364		6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.751	23.192	1.35	21692	2186	99	0.2103	0.2071	0.2077	0.2379	0.2388	39.6775

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	27.056
f_angle_d	1.088
f_chiral_restr	0.055
f_plane_restr	0.01
f_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	368
Solvent Atoms	89
Heterogen Atoms	247

Software

Software
Software Name	Purpose
Blu-Ice	data collection
HKL-2000	data processing
HKL-2000	data scaling
SHELX	phasing
PHENIX	refinement