3DB2

Crystal structure of a putative nadph-dependent oxidoreductase (dhaf_2064) from desulfitobacterium hafniense dcb-2 at 1.70 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	8.86	293	0.17M sodium acetate, 29.6% polyethylene glycol 4000, 15.0% Glycerol, 0.1M TRIS pH 8.86, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP	8.14	277	15.0% Glycerol, 26.7% polyethylene glycol 4000, 0.17M sodium acetate, 0.1M TRIS pH 8.14, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.616	α = 90
b = 104.616	β = 90
c = 173.372	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	100	CCD	ADSC QUANTUM 315	1m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing	2008-02-17
2	2	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-01-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5	0.978791	SSRL	BL1-5
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97956	SSRL	BL11-1

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
2	1.7	29.748	99.9	0.1	0.1	4.6	9.9		120878

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)
2	1.7	1.74	99.3		0.772	0.772	1	3.8	8703

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	FREE R	1.7	29.748	120817	120817	6076	100	0.142	0.14		0.174	RANDOM	29.353

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
s_similar_adp_cmpnt	0.074
s_non_zero_chiral_vol	0.051
s_anti_bump_dis_restr	0.043
s_zero_chiral_vol	0.041
s_from_restr_planes	0.029
s_angle_d	0.028
s_bond_d	0.009
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7986
Nucleic Acid Atoms
Solvent Atoms	598
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SHELXL-97	refinement
PHENIX	refinement
SHELX	phasing
SHELX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing
MolProbity	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.