3LYW | pdb_00003lyw

Crystal structure of YbbR family protein Dhaf_0833 from Desulfitobacterium hafniense DCB-2. Northeast Structural Genomics Consortium target id DhR29B

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	30% PEG3350, sodium acetate 10mM, 5% Glycerol, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.827	α = 90
b = 44.827	β = 90
c = 85.997	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	100	CCD	ADSC QUANTUM 4		2010-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.979	NSLS	X4A

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	1.8	50	99.6	0.058	0.054	14.5	17.7	15491	15491			26.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.83	100		0.412	0.43	24	13.4	768

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.9	25.52	2	12986	773	98.3	0.224	0.224	0.2395	0.258	0.2708	RANDOM	28.3

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]
-5.3			-5.3		10.6

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.9
c_angle_deg	1.6
c_improper_angle_d	0.77
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	669
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
SHELXS	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling