☰ Navigation Tabs
Crystal structure of fungal lipoxygenase from Fusarium graminearum. P212121 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 7 295 10% PEG3350, 0.05 M proline, 0.1 M imidazole acetate
Crystal Properties Matthews coefficient Solvent content 2.4 48.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.489 α = 90 b = 95.06 β = 90 c = 189.49 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 100 PIXEL DECTRIS PILATUS3 S 6M 2014-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.7413 APS 24-ID-C
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 47.58 98.5 0.072 0.993 8.2 6.2 40654 31.6
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 2.79 2.94 97.9 0.395 0.828 2.2 6.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3RDE 2.79 47.58 38588 2015 98.15 0.20763 0.20547 0.24943 0.2336 RANDOM 57.842
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] 8.29 -4.36 -3.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.922 r_dihedral_angle_4_deg 18.434 r_dihedral_angle_3_deg 16.118 r_dihedral_angle_1_deg 6.924 r_long_range_B_refined 2.547 r_long_range_B_other 2.547 r_mcangle_it 1.47 r_mcangle_other 1.47 r_angle_refined_deg 1.314 r_scangle_other 1.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.922 r_dihedral_angle_4_deg 18.434 r_dihedral_angle_3_deg 16.118 r_dihedral_angle_1_deg 6.924 r_long_range_B_refined 2.547 r_long_range_B_other 2.547 r_mcangle_it 1.47 r_mcangle_other 1.47 r_angle_refined_deg 1.314 r_scangle_other 1.217 r_angle_other_deg 1.13 r_mcbond_it 0.821 r_mcbond_other 0.82 r_scbond_it 0.699 r_scbond_other 0.697 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10103 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing