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Crystal structure of agmatine coumaroyltransferase from Triticum aestivum
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 0.2352 0.2564 0.2566 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
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