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Agrocybe pediades linalool sunthase (Ap.LS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PS1 1ps1, 2wbu experimental model PDB 2WBU 1ps1, 2wbu
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295.15 10mM MgCl2, 0.2 M Sodium citrate tribasic dihydrate pH 5.6, 2% v/v Tacsimate pH 5 and 18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.925 α = 90 b = 80.665 β = 96.05 c = 69.906 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2021-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.98 50 90.5 0.089 29.7 5.8 48065
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.01 0.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MAD FREE R-VALUE 1ps1, 2wbu 1.988 46.804 44039 1831 82.681 0.217 0.2144 0.2745 0.2831 66.281
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] 3.179 0.546 -6.036 2.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.4 r_dihedral_angle_3_deg 19.269 r_dihedral_angle_4_deg 17.85 r_lrange_other 11.69 r_lrange_it 11.68 r_scangle_it 8.904 r_scangle_other 8.903 r_mcangle_other 8.682 r_mcangle_it 8.681 r_mcbond_it 6.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.4 r_dihedral_angle_3_deg 19.269 r_dihedral_angle_4_deg 17.85 r_lrange_other 11.69 r_lrange_it 11.68 r_scangle_it 8.904 r_scangle_other 8.903 r_mcangle_other 8.682 r_mcangle_it 8.681 r_mcbond_it 6.171 r_mcbond_other 6.168 r_scbond_it 6.093 r_scbond_other 6.092 r_dihedral_angle_1_deg 5.734 r_angle_refined_deg 1.448 r_angle_other_deg 1.299 r_xyhbond_nbd_refined 0.259 r_nbd_other 0.246 r_symmetry_xyhbond_nbd_refined 0.23 r_nbd_refined 0.208 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.13 r_symmetry_xyhbond_nbd_other 0.12 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5049 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MADSYS phasing