4JYL | pdb_00004jyl

Crystal structure of enoyl-CoA hydratase from Thermoplasma volcanium GSS1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	289	1 ul of 15.3 mg/ml protein in 20mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5mM TCEP were mixed with 1 ul of The Cryos Suite condition #26 (0.07 M tri-Sodium citrate pH 5.6, 0.7 M Ammonium phosphate, 30% (v/v) Glycerol) and equilibrated against 1.9 M NaCl in QIAGEN EasyXtal 15-Well Tool plate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.102	α = 90
b = 117.229	β = 91.43
c = 91.505	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 225 mm CCD	C(111)	2013-03-06	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)	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	2.37	50	99.8	0.165	0.165	15.2	5.6	68626	68489		-3	36.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.37	2.41	99.1		0.68	0.68	1.9	3.7	3387

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 (All)	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	2.37	45.78	68596	68445	3464	99.78	0.1589	0.1589	0.1573	0.17	0.1905	0.2	RANDOM	31.6749

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]
-1.24		1.64	-0.47		1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.022
r_dihedral_angle_4_deg	20.982
r_dihedral_angle_3_deg	16.542
r_dihedral_angle_1_deg	5.953
r_angle_refined_deg	1.717
r_angle_other_deg	1.372
r_chiral_restr	0.092
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.009
r_gen_planes_other	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11247
Nucleic Acid Atoms
Solvent Atoms	667
Heterogen Atoms	11

Software

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