☰ Navigation Tabs
The 2.6 A crystal structure of the lipoxygenase domain of human arachidonate 12-lipoxygenase, 12S-type
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LOX PDB entry 1LOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 1.0M LiCl2, 0.1M Citric acid pH 4.0, 20% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.59 α = 65.37 b = 70.153 β = 88.01 c = 77.868 γ = 69.82
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2007-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97627 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2.6 47.193 97.8 0.158 0.158 10.3 3.5 32115 31408 2 31.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.74 97.2 0.509 0.509 3.3 3.5 4642
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1LOX 2.6 47.19 31119 30444 1628 97.83 0.20976 0.20625 0.2104 0.2757 0.2791 RANDOM 20.945
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] 0.07 0.02 -0.06 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.866 r_dihedral_angle_4_deg 21.189 r_dihedral_angle_3_deg 16.592 r_dihedral_angle_1_deg 8.685 r_scangle_it 1.383 r_angle_refined_deg 1.309 r_angle_other_deg 0.968 r_scbond_it 0.907 r_mcangle_it 0.62 r_mcbond_it 0.531
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.866 r_dihedral_angle_4_deg 21.189 r_dihedral_angle_3_deg 16.592 r_dihedral_angle_1_deg 8.685 r_scangle_it 1.383 r_angle_refined_deg 1.309 r_angle_other_deg 0.968 r_scbond_it 0.907 r_mcangle_it 0.62 r_mcbond_it 0.531 r_symmetry_hbond_refined 0.365 r_xyhbond_nbd_refined 0.238 r_symmetry_vdw_other 0.233 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.203 r_nbd_other 0.187 r_nbtor_refined 0.184 r_chiral_restr 0.149 r_nbtor_other 0.088 r_metal_ion_refined 0.079 r_mcbond_other 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7160 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection XDS data reduction SCALA data scaling MOLREP phasing