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REFINED STRUCTURE OF SOYBEAN LIPOXYGENASE-3 WITH 4-NITROCATECHOL AT 2.15 ANGSTROM RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BYT PDB ENTRY 1BYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 295 20% PEG 8000, citrate-phosphate buffer 0.05M, tris.HCl, 0.2% sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.33 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.905 α = 90 b = 137.531 β = 95.48 c = 61.88 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 295 IMAGE PLATE RIGAKU RAXIS IV Focusing mirrors 1997-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.15 40 0.988 0.079 13.7 2 50978 50343 34.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 0.993 0.346 2.14 2 5046
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 (All) 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 1BYT 2.15 10 49989 47446 2543 99.08 0.1887 0.1887 0.1863 0.2326 0.2401 RANDOM 26.82
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] 0.91 0.97 0.63 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.451 r_scangle_it 4.163 r_scbond_it 2.902 r_angle_refined_deg 1.979 r_mcangle_it 1.652 r_mcbond_it 0.929 r_symmetry_hbond_refined 0.298 r_xyhbond_nbd_refined 0.202 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.451 r_scangle_it 4.163 r_scbond_it 2.902 r_angle_refined_deg 1.979 r_mcangle_it 1.652 r_mcbond_it 0.929 r_symmetry_hbond_refined 0.298 r_xyhbond_nbd_refined 0.202 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.148 r_chiral_restr 0.13 r_bond_refined_d 0.016 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6799 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CCP4 phasing