3KQ8 | pdb_00003kq8

5-Te-uridine derivatized DNA-8mer

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	10% v / v MPD, 40 mM Na Cacodylate pH 7.0, 12 mM Spermine tetra-HCl, 80 mM Potassium Chloride and 20 mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2	38.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.242	α = 90
b = 42.242	β = 90
c = 23.929	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	99	CCD	ADSC QUANTUM 210		2009-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	1.54	NSLS	X12C

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	1.6	50	99.2	0.074	49.77	22.5	3147	3122

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)
	1.6	1.63	93.4		0.186	15.5	7.8	141

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.6	29.87	2994	2965	134	99.04	0.18864	0.18643	0.2904	0.22911	0.3037	RANDOM	15.594

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]
-0.04			-0.04		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.531
r_scangle_it	1.438
r_scbond_it	1.154
r_metal_ion_refined	0.993
r_nbtor_refined	0.273
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.177
r_nbd_refined	0.139
r_symmetry_hbond_refined	0.1
r_chiral_restr	0.052
r_gen_planes_refined	0.009
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	162
Solvent Atoms	36
Heterogen Atoms	1

Software

Software
Software Name	Purpose
CBASS	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling