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Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin F1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other apo PCY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 PCY1-S562A complex with PresegF1 was crystallized at 13.0 mg/mL with 0.161.3 mM PresegB1 in 27% (w/v) PEG 3350, 100 mM Ca chloride and 0.1 M Bis-Tris at pH 6.5. For cryo protection 10 % (v/v) glycerol were added to reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.17 43.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.86 α = 87.64 b = 85.82 β = 78.32 c = 137.87 γ = 89.52
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 PILATUS3 6M 2016-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9785 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.86 73.72 95.8 7.8 3.4 222236
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT apo PCY1 1.86 73.72 222236 11725 95.75 0.19445 0.19295 0.2006 0.22338 0.2294 RANDOM 27.171
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] -0.58 0.79 0.63 0.27 -0.75 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.177 r_dihedral_angle_4_deg 17.865 r_dihedral_angle_3_deg 12.381 r_long_range_B_other 6.682 r_long_range_B_refined 6.678 r_dihedral_angle_1_deg 6.333 r_scangle_other 4.988 r_scbond_it 3.337 r_scbond_other 3.337 r_mcangle_it 2.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.177 r_dihedral_angle_4_deg 17.865 r_dihedral_angle_3_deg 12.381 r_long_range_B_other 6.682 r_long_range_B_refined 6.678 r_dihedral_angle_1_deg 6.333 r_scangle_other 4.988 r_scbond_it 3.337 r_scbond_other 3.337 r_mcangle_it 2.815 r_mcangle_other 2.815 r_mcbond_it 1.889 r_mcbond_other 1.888 r_angle_refined_deg 1.441 r_angle_other_deg 0.938 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23233 Nucleic Acid Atoms Solvent Atoms 930 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing