5BSW

Crystal structure of 4-coumarate:CoA ligase delta-V341 mutant complexed with feruloyl adenylate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	280	AMP-CoA complex (DV341 mutant): 25% (w/v) PEG 3350, 0.2 M ammonium acetate, 0.1 M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.276	α = 90
b = 97.186	β = 90
c = 124.793	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	MAR CCD 130 mm		2010-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97856	APS	21-ID-F

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	2.1	50	97.9	0.099	6.5	8.1		65538

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	2.1	2.18	86		0.469		6	5682

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.1	25	62119	3302	97.93	0.1992	0.1967	0.2464	RANDOM	28.031

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]
2.62			-1.2		-1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.166
r_dihedral_angle_4_deg	18.777
r_dihedral_angle_3_deg	15.773
r_dihedral_angle_1_deg	5.922
r_scangle_it	2.873
r_scbond_it	1.747
r_angle_refined_deg	1.362
r_mcangle_it	1.171
r_mcbond_it	0.631
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.166
r_dihedral_angle_4_deg	18.777
r_dihedral_angle_3_deg	15.773
r_dihedral_angle_1_deg	5.922
r_scangle_it	2.873
r_scbond_it	1.747
r_angle_refined_deg	1.362
r_mcangle_it	1.171
r_mcbond_it	0.631
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8120
Nucleic Acid Atoms
Solvent Atoms	571
Heterogen Atoms	72

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.