4HQI | pdb_00004hqi

Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	20 mM sodium cacodylate (pH 7.0), 6 mM spermine tetra-HCl, 20 mM LiCl, 40 mM SrCl2 and 5% v/v 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 291K
2	VAPOR DIFFUSION, HANGING DROP	7	291	20 mM sodium cacodylate (pH 7.0), 6 mM spermine tetra-HCl, 40 mM KCl, 10 mM BaCl2 and 5% v/v 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.384	α = 90
b = 36.774	β = 90
c = 77.653	γ = 90

Symmetry
Space Group	P 21 21 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	MARMOSAIC 300 mm CCD	Si(111)	2009-07-17	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 300 mm CCD	C(111)	2008-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.60499	APS	21-ID-D
2	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

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	1.7	30	93.4	0.044	52.33	6.4	8811	8236		5

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)
1,2	1.7	1.76			0.228	5.65	4	524

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	SAD	THROUGHOUT	1.7	20.67	7486	734	93.39	0.26227	0.25885	0.2554	0.29823	0.291	RANDOM	44.14

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]
3.33			1.38		-4.71

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.652
r_chiral_restr	0.125
r_gen_planes_refined	0.023
r_bond_refined_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	481
Solvent Atoms	49
Heterogen Atoms	15

Software

Software
Software Name	Purpose
MD2	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing