3L77

X-ray structure alcohol dehydrogenase from archaeon Thermococcus sibiricus complexed with 5-hydroxy-NADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JAP	PDB CODE 2JAP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	293	The reservoir solutions consisted of 0.1M Hepes pH 7.5, 0.2M sodium chloride, 25% w/v PEG 3350. The crystallization drop contained 2 μl of TsAdh319 solution (10 mg/ml) in 25 мМ Tris-HCl and 300 мМ NaCl, рН 7.5, and 2 μl reservoir solution. Crystals of dimensions 0.4 x 0.1 x 0.06 mm were obtained after 3-4 weeks. VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.62	α = 90
b = 83.23	β = 90
c = 120.75	γ = 90

Symmetry
Space Group	I 2 2 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	IMAGE PLATE	MAR555 FLAT PANEL		2009-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

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	1.55	20	87.3	0.102	0.087	18.45			35365

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	1.55	1.6	78.8		0.775	2.27

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB CODE 2JAP	1.55	19.67	2.35	35365	1061	86.1	0.134	0.133	0.13	0.18	0.17

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]
5.9327			-2.5237		-3.529

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.42
f_angle_d	1.186
f_chiral_restr	0.106
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1854
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	118

Software

Software
Software Name	Purpose
PHENIX	refinement
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.