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Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin B1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 PCY1-S562A complex with PresegB1 was crystallized at 13.3 mg/mL with 0.163 mM PresegB1 in 34.5% (w/v) PEG 3350 and 70 mM Mg sulfate. For cryo protection 5 % (v/v) glycerol were added to reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.35 47.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.86 α = 90 b = 65.2 β = 95.91 c = 140.17 γ = 90
Symmetry Space Group P 1 2 1
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 PILATUS 6M-F 2016-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
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 2.17 47.62 99.5 10.9 3.4 80090
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.17 47.62 80090 4273 99.44 0.21732 0.21572 0.2206 0.24803 0.2512 RANDOM 44.405
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] 3.19 0.38 -0.2 -3.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.337 r_dihedral_angle_4_deg 15.929 r_dihedral_angle_3_deg 12.778 r_dihedral_angle_1_deg 6.182 r_long_range_B_refined 5.252 r_long_range_B_other 5.252 r_scangle_other 2.858 r_mcangle_other 2.116 r_mcangle_it 2.115 r_scbond_it 1.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.337 r_dihedral_angle_4_deg 15.929 r_dihedral_angle_3_deg 12.778 r_dihedral_angle_1_deg 6.182 r_long_range_B_refined 5.252 r_long_range_B_other 5.252 r_scangle_other 2.858 r_mcangle_other 2.116 r_mcangle_it 2.115 r_scbond_it 1.813 r_scbond_other 1.779 r_mcbond_it 1.3 r_mcbond_other 1.296 r_angle_refined_deg 1.257 r_angle_other_deg 0.919 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11692 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing