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Crystal structure of fungal lipoxygenase from Fusarium graminearum. P21 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 8.46 295 22% PEG3350, 0.3 M ammonium acetate, 0.1 M Tris
Crystal Properties Matthews coefficient Solvent content 2.05 40.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.007 α = 90 b = 94.769 β = 106.16 c = 105.076 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 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) 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 3.3 40 99.5 0.057 9.7 3 20760 81.6
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 3.3 3.56 99.8 0.425 0.763 1.9 2.9
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 3RDE 3.3 40 20082 664 99.41 0.19536 0.19382 0.1934 0.24118 0.2336 RANDOM 110.595
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] -1.41 2.74 -1.86 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.716 r_dihedral_angle_3_deg 16.033 r_dihedral_angle_4_deg 14.024 r_dihedral_angle_1_deg 6.478 r_mcangle_it 2.901 r_mcangle_other 2.901 r_scangle_other 2.21 r_mcbond_it 1.662 r_mcbond_other 1.661 r_scbond_it 1.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.716 r_dihedral_angle_3_deg 16.033 r_dihedral_angle_4_deg 14.024 r_dihedral_angle_1_deg 6.478 r_mcangle_it 2.901 r_mcangle_other 2.901 r_scangle_other 2.21 r_mcbond_it 1.662 r_mcbond_other 1.661 r_scbond_it 1.209 r_scbond_other 1.209 r_angle_refined_deg 1.182 r_angle_other_deg 1.178 r_chiral_restr 0.047 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10534 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing