4ILK | pdb_00004ilk

Crystal structure of short chain alcohol dehydrogenase (rspB) from E. coli CFT073 (EFI TARGET EFI-506413) complexed with cofactor NADH

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	282	Protein solution was at 10 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl and 50 mM imidazole. Mother liqueur contained 0.2 M ammonium chloride, 0.01 M calcium chloride dihydrate, 0.05 M Tris (pH 8.5), 30% PEG 4,000. Cryoprotectant was 13% glycerol, vapor diffusion, sitting drop, temperature 282K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.322	α = 90
b = 97.133	β = 90
c = 144.101	γ = 90

Symmetry
Space Group	P 21 21 21

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	RAYONIX MX-225		2012-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	30	99.6	0.088	9	7.6	45647	45465

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	2.07	99.8		0.777		7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.003	29.533	1.36	45600	41885	2112	91.89	0.1675	0.1648	0.16	0.2177	0.21

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]
-0.7191			1.4606		-0.7415

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.668
f_angle_d	1.172
f_chiral_restr	0.075
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5100
Nucleic Acid Atoms
Solvent Atoms	387
Heterogen Atoms	92

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

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.