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Crystal structure of fungal lipoxygenase from Fusarium graminearum. 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 7.46 295 25% PEG3350, 0.3 M ammonium acetate, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.963 α = 90 b = 121.116 β = 95.13 c = 102.122 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 CCD MAR CCD 165 mm MIRRORS 2016-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 1.38079 CAMD GCPCC
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 2.4 40 99.7 0.083 9.6 3.7 55511 20.4
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 2.4 2.49 97.8 0.359 0.71 1.7 3.3
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 2.4 35.4 54372 1139 99.69 0.19098 0.19032 0.1946 0.22087 0.2228 RANDOM 31.878
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] -0.02 0.78 -0.7 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.561 r_dihedral_angle_4_deg 17.088 r_dihedral_angle_3_deg 15.894 r_dihedral_angle_1_deg 6.529 r_long_range_B_refined 3.067 r_long_range_B_other 3.066 r_mcangle_it 1.495 r_mcangle_other 1.495 r_angle_refined_deg 1.27 r_angle_other_deg 1.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.561 r_dihedral_angle_4_deg 17.088 r_dihedral_angle_3_deg 15.894 r_dihedral_angle_1_deg 6.529 r_long_range_B_refined 3.067 r_long_range_B_other 3.066 r_mcangle_it 1.495 r_mcangle_other 1.495 r_angle_refined_deg 1.27 r_angle_other_deg 1.169 r_scangle_other 1.001 r_mcbond_it 0.813 r_mcbond_other 0.81 r_scbond_it 0.551 r_scbond_other 0.551 r_chiral_restr 0.054 r_bond_refined_d 0.005 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 10757 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing