7CYS | pdb_00007cys

Crystal structure of barley agmatine coumaroyltransferase (HvACT), an N-acyltransferase in BAHD superfamily

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6DD2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.08 M sodium cacodylate, pH 6.5, 0.16 M magnesium acetate, 16% (w/v) polyethylene glycol 8,000, and 20% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.632	α = 90
b = 59.521	β = 91.285
c = 73.627	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	95	PIXEL	DECTRIS PILATUS3 S 6M		2020-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.81	50	97.8	0.036	0.999	16.3	3.1		44594

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.81	1.85	82.5		0.914	2.2	2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6dd2	1.81	46.326	44578	2175	97.746	0.191	0.1906	0.2	0.2033	0.21	23.607

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]
-1.252		0.11	0.691		0.556

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.366
r_dihedral_angle_4_deg	13.664
r_dihedral_angle_3_deg	12.828
r_dihedral_angle_1_deg	5.923
r_lrange_it	3.953
r_lrange_other	3.912
r_scangle_it	2.609
r_scangle_other	2.609
r_mcangle_it	2.166
r_mcangle_other	2.166
r_scbond_it	1.587
r_scbond_other	1.586
r_angle_refined_deg	1.354
r_mcbond_it	1.287
r_mcbond_other	1.287
r_angle_other_deg	1.257
r_symmetry_nbd_refined	0.205
r_nbd_refined	0.198
r_symmetry_nbd_other	0.18
r_nbd_other	0.164
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.095
r_symmetry_xyhbond_nbd_refined	0.094
r_symmetry_nbtor_other	0.078
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3304
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MoRDa	phasing