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Crystal structure of onion lachrymatory factor synthase (LFS) containing 1,2-propanediol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GTF PDB entry 5GTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Ammonium sulfate, MES
Crystal Properties Matthews coefficient Solvent content 3.04 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.858 α = 90 b = 172.858 β = 90 c = 64.91 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2016-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 1.7 50 97.3 19.8 6.1 204662
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 79.1 0.86 4.2 4.9
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 (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 PDB entry 5GTF 1.7 47.94 194424 10237 97.28 0.23128 0.22977 0.2364 0.25979 0.2613 RANDOM 20.053
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] 5.77 5.77 -11.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.841 r_dihedral_angle_4_deg 22.504 r_dihedral_angle_3_deg 18.479 r_dihedral_angle_1_deg 9.388 r_long_range_B_refined 5.031 r_long_range_B_other 5.024 r_scangle_other 3.594 r_mcangle_it 3.283 r_mcangle_other 3.283 r_angle_refined_deg 2.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.841 r_dihedral_angle_4_deg 22.504 r_dihedral_angle_3_deg 18.479 r_dihedral_angle_1_deg 9.388 r_long_range_B_refined 5.031 r_long_range_B_other 5.024 r_scangle_other 3.594 r_mcangle_it 3.283 r_mcangle_other 3.283 r_angle_refined_deg 2.821 r_scbond_it 2.753 r_scbond_other 2.753 r_mcbond_it 2.534 r_mcbond_other 2.532 r_angle_other_deg 1.416 r_chiral_restr 0.187 r_bond_refined_d 0.031 r_gen_planes_refined 0.016 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 9640 Nucleic Acid Atoms Solvent Atoms 584 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing