4JYJ | pdb_00004jyj

Crystal Structure of putative enoyl-CoA hydratase/isomerase from Novosphingobium aromaticivorans DSM 12444

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	The drop was a mixture of 200 nl of 21.23 ml/ml protein with 200 nL of Hampton Research's Index HT condition G1 (25% PEG 3350, 200 mM NaCl, 100 mM Tris pH 8.5) equalibrated against a reservoir of 2.5 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.81	31.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.697	α = 90
b = 112.697	β = 90
c = 112.697	γ = 90

Symmetry
Space Group	P 21 3

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		2013-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97920	APS	19-BM

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	2.2	40	99.4	0.115		5		24422

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.24	98.2		1.72	5.4	1177

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	2.2	33.98	23109	1247	99.44	0.1569	0.1542	0.16	0.2069	0.21	RANDOM	39.3482

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]
-15.02	0.81	0.36	2.39	-29.84	12.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.273
r_dihedral_angle_4_deg	20.294
r_dihedral_angle_3_deg	16.131
r_dihedral_angle_1_deg	6.17
r_angle_refined_deg	1.871
r_angle_other_deg	1.158
r_chiral_restr	0.104
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.273
r_dihedral_angle_4_deg	20.294
r_dihedral_angle_3_deg	16.131
r_dihedral_angle_1_deg	6.17
r_angle_refined_deg	1.871
r_angle_other_deg	1.158
r_chiral_restr	0.104
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4007
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	10

Software

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

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.