5VE2 | pdb_00005ve2

Crystal structure of enoyl-CoA hydratase/isomerase from Pseudoalteromonas atlantica T6c at 2.3 A resolution.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.2 ul of 20 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 JCSG+ condition #89 (0.2M ammonium acetate, 0.1M Bis-Tris pH 5.5, 45% (v/v) MPD) and equilibrated against 0.9 M NaCl solution in 96 Well 3 drop Crystallization Plate (SwissCi).

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.66	α = 90
b = 160.141	β = 90.12
c = 136.271	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	MARMOSAIC 300 mm CCD	Beryllium Lenses	2013-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.987	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.3	38	95.2	0.084	0.084	0.103	0.059	6	3		142189		-3	37.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	97.5		0.336	0.336	0.409	0.23	0.933	3.3	3.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.3	38	134973	7178	95.14	0.2079	0.2051	0.2181	0.2576	0.2644	RANDOM	47.067

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]
-2.59		-0.05	1.25		1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.677
r_dihedral_angle_4_deg	18.907
r_dihedral_angle_3_deg	12.211
r_dihedral_angle_1_deg	5.345
r_angle_refined_deg	1.436
r_angle_other_deg	0.96
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.677
r_dihedral_angle_4_deg	18.907
r_dihedral_angle_3_deg	12.211
r_dihedral_angle_1_deg	5.345
r_angle_refined_deg	1.436
r_angle_other_deg	0.96
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22496
Nucleic Acid Atoms
Solvent Atoms	1998
Heterogen Atoms	67

Software

Software
Software Name	Purpose
MD2	data collection
HKL-3000	data scaling
SHELXD	phasing
DM	phasing
MLPHARE	phasing
HKL-3000	phasing
BUCCANEER	model building
REFMAC	refinement
HKL-3000	data reduction
DENZO	data reduction
SCALEPACK	data scaling

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.