3GEK

Crystal structure of putative thioesterase yhdA from Lactococcus lactis. Northeast Structural Genomics Consortium Target KR113

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	14% PEG 3350, 20% Ethylene glycol, 0.2M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.948	α = 90
b = 64.056	β = 90
c = 144.657	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	ADSC QUANTUM 4	mirrors	2009-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.979	NSLS	X4A

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	2.24	50	98.7	0.069	27.8	7.6		51899		-3

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	2.24	2.32	87.7		0.41	6.3	7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1VH5	2.24	46.18	27547	1385	100	0.2253	0.22366	0.25548	RANDOM	51.656

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]
-4.98			4.53		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.95
r_dihedral_angle_3_deg	15.474
r_dihedral_angle_4_deg	9.405
r_dihedral_angle_1_deg	5.916
r_scangle_it	1.327
r_angle_refined_deg	1.065
r_scbond_it	0.897
r_mcangle_it	0.711
r_mcbond_it	0.541
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.186
r_nbd_refined	0.184
r_symmetry_hbond_refined	0.164
r_xyhbond_nbd_refined	0.105
r_chiral_restr	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3917
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing