4WCZ

Crystal structure of a putative enoyl-CoA hydratase/isomerase from Novosphingobium aromaticivorans

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	0.2 ul of mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the Hampton Index HT #65 (F5) (0.1 M Ammonium acetate, 0.1 M BIS_TRIS pH 5.5, 17% (w/v) Polyethylene glycol 10,000) and equilibrated against 1.25 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.

Crystal Properties
Matthews coefficient	Solvent content
2.46	45.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.636	α = 90
b = 128.469	β = 116.36
c = 84.467	γ = 90

Symmetry
Space Group	P 1 21 1

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 210r		2013-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97936	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.82	50	99.5	0.104	0.114	0.054	10	4.7		138544

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.85	93.8		0.598	0.49		3.6	6515

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	1.82	50	138432	6926	99.16	0.1685	0.1672	0.1926	RANDOM	26.527

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]
1.26		0.09	-0.6		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.921
r_dihedral_angle_4_deg	16.405
r_dihedral_angle_3_deg	11.17
r_dihedral_angle_1_deg	5.015
r_mcangle_it	1.253
r_angle_refined_deg	1.008
r_mcbond_it	0.74
r_mcbond_other	0.74
r_angle_other_deg	0.713
r_chiral_restr	0.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.921
r_dihedral_angle_4_deg	16.405
r_dihedral_angle_3_deg	11.17
r_dihedral_angle_1_deg	5.015
r_mcangle_it	1.253
r_angle_refined_deg	1.008
r_mcbond_it	0.74
r_mcbond_other	0.74
r_angle_other_deg	0.713
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11180
Nucleic Acid Atoms
Solvent Atoms	1491
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing

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.