4K02 | pdb_00004k02

Crystal structure of AtDHNAT1, a 1,4-dihydroxy-2-naphthoyl-CoA thioesterase from Arabidopsis thaliana

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SC0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	2.7 M NaHCOOH, 100 mM Tris-HCl, 10 mM n-octyl- D-glucoside in protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.529	α = 90
b = 99.529	β = 90
c = 61.257	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	110	CCD	MARMOSAIC 300 mm CCD		2012-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D

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	28.88	96.4	0.058	48.8	35.3	26984	26984

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	1.9	1.95	84.1		0.764	2.4	22.5

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	1SC0	1.9	28.88	26702	26702	1361	95.65	0.18451	0.18451	0.18318	0.19	0.21055	0.22	RANDOM	63.246

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]
-1.2	-1.2		-1.2		3.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.344
r_dihedral_angle_4_deg	22.782
r_dihedral_angle_3_deg	16.24
r_dihedral_angle_1_deg	8.583
r_angle_refined_deg	1.618
r_angle_other_deg	0.842
r_chiral_restr	0.108
r_gen_planes_refined	0.011
r_bond_refined_d	0.008
r_gen_planes_other	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.344
r_dihedral_angle_4_deg	22.782
r_dihedral_angle_3_deg	16.24
r_dihedral_angle_1_deg	8.583
r_angle_refined_deg	1.618
r_angle_other_deg	0.842
r_chiral_restr	0.108
r_gen_planes_refined	0.011
r_bond_refined_d	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1914
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms

Software

Software
Software Name	Purpose
JBluIce-EPICS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.