3BJK | pdb_00003bjk

Crystal structure of HI0827, a hexameric broad specificity acyl-coenzyme A thioesterase: The Asp44Ala mutant enzyme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YLI	PDB entry 1YLI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	Reservoir: 30% Saturated sodium citrate, 100 mM Hepes pH 7.5, 5% Ethylene glycol. Protein solution: 16 mg/mL protein in 10 mM Hepes pH 7.5, 150 mM KCl. Hanging drops: 1:1 reservoir and protein solutions. Cryoprotection: increasing ethylene glycol concentration to 18% under perfluoropolyether oil coat, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.487	α = 90
b = 63.108	β = 100.14
c = 104.718	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	IMAGE PLATE	RIGAKU RAXIS IV++	Osmic mirrors	2003-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.9	30	98	0.065	8.2	6.1	79693	79693

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1YLI	1.9	29.88	78077	78077	6353	99.94	0.172	0.172	0.169	0.18	0.21	0.22	RANDOM	31.365

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]
-0.12		-0.57	0.78		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.139
r_dihedral_angle_4_deg	16.755
r_dihedral_angle_3_deg	15.746
r_dihedral_angle_1_deg	6.183
r_scangle_it	3.697
r_scbond_it	2.424
r_angle_refined_deg	1.662
r_mcangle_it	1.54
r_mcbond_it	1.106
r_angle_other_deg	0.839
r_mcbond_other	0.273
r_symmetry_vdw_other	0.242
r_symmetry_vdw_refined	0.221
r_xyhbond_nbd_refined	0.198
r_nbd_refined	0.197
r_nbd_other	0.184
r_symmetry_hbond_refined	0.169
r_nbtor_refined	0.165
r_chiral_restr	0.097
r_nbtor_other	0.085
r_bond_refined_d	0.019
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6366
Nucleic Acid Atoms
Solvent Atoms	463
Heterogen Atoms	139

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing