1TBU

Crystal structure of N-terminal domain of yeast peroxisomal thioesterase-1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	294	1.5 M sodium formate, 0.1 M sodium citrate buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.261	α = 90
b = 80.261	β = 90
c = 137.079	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	ADSC QUANTUM 4	mirrors	2001-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B	0.9149	NSLS	X9B

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		0.058	21.9	4.2		26378		-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)
	2.2	2.26	99.8		0.225	2.8	3.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	2.2	12	25524	25524	852	100	0.21609	0.21609	0.21461	0.2603	RANDOM	36.155

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]
-0.21	-0.11		-0.21		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	9.51
r_scangle_it	4.26
r_scbond_it	2.568
r_mcangle_it	2.282
r_angle_refined_deg	1.835
r_mcbond_it	1.243
r_angle_other_deg	0.946
r_nbd_refined	0.271
r_nbd_other	0.26
r_xyhbond_nbd_refined	0.206
r_symmetry_vdw_other	0.201
r_symmetry_vdw_refined	0.169
r_chiral_restr	0.12
r_nbtor_other	0.096
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_gen_planes_other	0.01
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_refined
r_symmetry_hbond_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	3101
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SHELXD	phasing
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction