3KD9

Crystal structure of pyridine nucleotide disulfide oxidoreductase from Pyrococcus horikoshii

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	45% MPD, 200mM Ammonium Acetate, 100mM Bis-Tris (pH 5.5), VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.81	α = 90
b = 114.81	β = 90
c = 353.917	γ = 90

Symmetry
Space Group	P 41 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 315	mirrors	2009-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9290	NSLS	X29A

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	2.75	50	99.3	0.09	7.1	34.2	62345	62345			55.7

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	2.75	2.8	97.3		0.6	3	33.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.75	49.31	62345	60259	1827	96.3	0.244	0.244	0.284	RANDOM	52

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]
-2.35			-2.35		4.69

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.9
c_scangle_it	2.9
c_mcangle_it	1.86
c_scbond_it	1.85
c_angle_deg	1.5
c_mcbond_it	1.13
c_improper_angle_d	0.92
c_bond_d	0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9443
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	6

Software

Software
Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
Coot	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling