☰ Navigation Tabs
Crystal structure of fungal lipoxygenase from Fusarium graminearum. Second C2 crystal form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RDE PDB entry 3RDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 295 22% PEG3350, 0.3 M ammonium acetate, 0.1 M Tris
Crystal Properties Matthews coefficient Solvent content 2.05 40.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.365 α = 90 b = 113.671 β = 90.25 c = 99.437 γ = 90
Symmetry Space Group C 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 EIGER X 16M MIRRORS 2016-12-12 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) Rpim I (All) CC (Half) 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 2.79 83.59 100 0.076 0.992 8.6 3.8 33864 41.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.94 100 0.428 0.581 1.9 3.6
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 3RDE 2.79 64.08 32762 1089 98.77 0.1768 0.17481 0.1757 0.2372 0.2354 RANDOM 47.232
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] -25.46 -1.88 -23.98 49.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.676 r_dihedral_angle_4_deg 18.73 r_dihedral_angle_3_deg 17.35 r_dihedral_angle_1_deg 6.469 r_long_range_B_refined 2.498 r_long_range_B_other 2.495 r_angle_refined_deg 1.528 r_mcangle_it 1.476 r_mcangle_other 1.476 r_scangle_other 1.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.676 r_dihedral_angle_4_deg 18.73 r_dihedral_angle_3_deg 17.35 r_dihedral_angle_1_deg 6.469 r_long_range_B_refined 2.498 r_long_range_B_other 2.495 r_angle_refined_deg 1.528 r_mcangle_it 1.476 r_mcangle_other 1.476 r_scangle_other 1.218 r_angle_other_deg 1.031 r_mcbond_it 0.848 r_mcbond_other 0.848 r_scbond_it 0.767 r_scbond_other 0.767 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 10587 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing