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Crystal structure of Arabidopsis thaliana COSY in complex with scopoletin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298.15 50 mM calcium acetate, 0.1 M sodium cacodylate pH 6.5, 20% glycerol, 500 uM coenzyme-A, 5 mg/mL protein
Crystal Properties Matthews coefficient Solvent content 2.53 51.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.514 α = 90 b = 88.886 β = 90 c = 96.901 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 PIXEL DECTRIS EIGER X 16M 2018-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9791 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.26 65.5 97.02 0.999 12.69 2 23643
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.341 90.69 0.7622 0.7622 0.425 0.89 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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8DQO 2.26 65.5 22455 1189 97.21 0.19636 0.19122 0.29135 0.2667 RANDOM 52.561
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] 2.84 -2.67 -0.17
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.952 r_dihedral_angle_2_deg 36.189 r_dihedral_angle_4_deg 20.86 r_dihedral_angle_3_deg 18.709 r_sphericity_bonded 18.213 r_dihedral_angle_1_deg 7.691 r_long_range_B_refined 5.644 r_long_range_B_other 5.629 r_mcangle_other 4.81 r_mcangle_it 4.806
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.952 r_dihedral_angle_2_deg 36.189 r_dihedral_angle_4_deg 20.86 r_dihedral_angle_3_deg 18.709 r_sphericity_bonded 18.213 r_dihedral_angle_1_deg 7.691 r_long_range_B_refined 5.644 r_long_range_B_other 5.629 r_mcangle_other 4.81 r_mcangle_it 4.806 r_scangle_other 4.744 r_scbond_it 3.792 r_scbond_other 3.79 r_mcbond_it 3.612 r_mcbond_other 3.594 r_rigid_bond_restr 1.86 r_angle_refined_deg 1.585 r_angle_other_deg 0.907 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3385 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing