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Crystal structure of the catalytic domain of porcine leukocyte 12-lipoxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P0M PDB ENTRY 2P0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 protein 6 mg/mL incubated with the solid OPP inhibitor for 16 hours, then further concentrated to 11~12 mg/mL in 10 mM Tris HCl, 1 mM TCEP, pH 7.4 buffer. reservoir solution: 0.1 M MES pH 6.5, 5%-10% PEG-20,000, 20% glycerol against 1 mL well solution of 0.1 M MES, 5%-10% PEG-20,000, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.68 54.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.45 α = 90 b = 181.54 β = 92.86 c = 91.61 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 CCD MARMOSAIC 300 mm CCD 2011-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0781 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.89 48.968 99.5 0.098 9 3.6 214779 214779
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) 1 1.89 1.99 98.3 0.284 0.284 2.4 3.4
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 2P0M 1.892 48.968 214717 6468 99.4 0.17323 0.17195 0.1788 0.21447 0.2181 RANDOM 17.665
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] 0.13 0.05 -0.17 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.678 r_dihedral_angle_4_deg 22.438 r_dihedral_angle_3_deg 14 r_dihedral_angle_1_deg 6.097 r_scangle_it 5.304 r_angle_other_deg 4.113 r_scbond_it 3.475 r_mcangle_it 2.244 r_angle_refined_deg 1.974 r_mcbond_it 1.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.678 r_dihedral_angle_4_deg 22.438 r_dihedral_angle_3_deg 14 r_dihedral_angle_1_deg 6.097 r_scangle_it 5.304 r_angle_other_deg 4.113 r_scbond_it 3.475 r_mcangle_it 2.244 r_angle_refined_deg 1.974 r_mcbond_it 1.337 r_chiral_restr 0.137 r_bond_refined_d 0.026 r_gen_planes_other 0.017 r_gen_planes_refined 0.012 r_bond_other_d 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17580 Nucleic Acid Atoms Solvent Atoms 1274 Heterogen Atoms 110
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOSFLM data reduction