7CYS

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6DD2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.08 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 coefficientSolvent content
2.4549.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.632α = 90
b = 59.521β = 91.285
c = 73.627γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95PIXELDECTRIS PILATUS3 S 6M2020-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.815097.80.0360.99916.33.144594
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.8582.50.9142.22

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6dd21.8146.32644578217597.7460.1910.19060.203323.607
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]
-1.2520.110.6910.556
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.366
r_dihedral_angle_4_deg13.664
r_dihedral_angle_3_deg12.828
r_dihedral_angle_1_deg5.923
r_lrange_it3.953
r_lrange_other3.912
r_scangle_it2.609
r_scangle_other2.609
r_mcangle_it2.166
r_mcangle_other2.166
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.366
r_dihedral_angle_4_deg13.664
r_dihedral_angle_3_deg12.828
r_dihedral_angle_1_deg5.923
r_lrange_it3.953
r_lrange_other3.912
r_scangle_it2.609
r_scangle_other2.609
r_mcangle_it2.166
r_mcangle_other2.166
r_scbond_it1.587
r_scbond_other1.586
r_angle_refined_deg1.354
r_mcbond_it1.287
r_mcbond_other1.287
r_angle_other_deg1.257
r_symmetry_nbd_refined0.205
r_nbd_refined0.198
r_symmetry_nbd_other0.18
r_nbd_other0.164
r_nbtor_refined0.159
r_xyhbond_nbd_refined0.128
r_chiral_restr0.095
r_symmetry_xyhbond_nbd_refined0.094
r_symmetry_nbtor_other0.078
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3304
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing