7DTP

Crystal structure of agmatine coumaroyltransferase from Triticum aestivum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7CYS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	100 mM MMT buffer pH 6.5, 25 % (w/v) PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.074	α = 90
b = 77.42	β = 90
c = 92.122	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	95	PIXEL	DECTRIS PILATUS3 S 6M		2020-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.000	Photon Factory	AR-NW12A

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	2.3	50	100	0.131	0.993	14.2	6.4		20776

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	100		0.927	0.782	1.9	6.6

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	7CYS	2.3	48.948	20727	1064	99.549	0.234	0.2331	0.24	0.2564	0.26	37.97

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]
-1.425			2.329		-0.904

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.621
r_dihedral_angle_3_deg	17.466
r_dihedral_angle_4_deg	12.777
r_dihedral_angle_1_deg	6.443
r_lrange_it	6.246
r_lrange_other	6.246
r_scangle_it	4.104
r_scangle_other	4.103
r_mcangle_it	3.364
r_mcangle_other	3.363
r_scbond_it	2.445
r_scbond_other	2.445
r_mcbond_it	2.139
r_mcbond_other	2.137
r_angle_refined_deg	1.342
r_angle_other_deg	1.136
r_nbd_other	0.23
r_nbd_refined	0.192
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.112
r_symmetry_xyhbond_nbd_refined	0.097
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.05
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_symmetry_xyhbond_nbd_other	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3123
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing