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Crystal structure of onion lachrymatory factor synthase (LFS), solute-free form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Ammonium sulfate, MES
Crystal Properties Matthews coefficient Solvent content 3.02 59.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.123 α = 90 b = 118.656 β = 90 c = 124.504 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 95 CCD ADSC QUANTUM 270 2015-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 50 99.6 15.2 6.7 66057
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 98
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 5GTF 2 50 62844 3213 99.59 0.19299 0.19093 0.1997 0.23327 0.2387 RANDOM 30.189
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] -0.04 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.747 r_dihedral_angle_4_deg 21.794 r_dihedral_angle_3_deg 16.093 r_long_range_B_refined 8.311 r_long_range_B_other 8.215 r_dihedral_angle_1_deg 6.872 r_scangle_other 5.77 r_scbond_it 3.842 r_scbond_other 3.841 r_mcangle_it 3.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.747 r_dihedral_angle_4_deg 21.794 r_dihedral_angle_3_deg 16.093 r_long_range_B_refined 8.311 r_long_range_B_other 8.215 r_dihedral_angle_1_deg 6.872 r_scangle_other 5.77 r_scbond_it 3.842 r_scbond_other 3.841 r_mcangle_it 3.095 r_mcangle_other 3.095 r_mcbond_it 2.308 r_mcbond_other 2.299 r_angle_refined_deg 1.852 r_angle_other_deg 0.863 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 4870 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing