3GDD | pdb_00003gdd

An inverted anthraquinone-DNA crystal structure

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	310	22 mM cacodylate, 0.8 mM magnesium chloride, 15 mM sodium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.698	α = 90
b = 29.698	β = 90
c = 60.883	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MAR CCD 165 mm		2002-05-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	0.907,0.921,0.920,0.861	ESRF	BM16

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.8	21.26	99.01	0.06	0.035		8.9	760	757		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.89	90.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.8	21.26	757	41	99.01	0.23335	0.23202	0.25	0.25926	0.27	RANDOM	40.12

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]
2.41			2.41		-4.82

RMS Deviations
Key	Refinement Restraint Deviation
r_mcbond_it	6.969
r_angle_refined_deg	1.769
r_scangle_it	1.06
r_scbond_it	0.651
r_nbtor_refined	0.338
r_nbd_refined	0.266
r_symmetry_vdw_refined	0.161
r_xyhbond_nbd_refined	0.137
r_symmetry_hbond_refined	0.09
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	164
Solvent Atoms	6
Heterogen Atoms	89

Software

Software
Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling