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Allene oxide synthase 8R-lipoxygenase from Plexaura homomalla
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FNQ PDB entries 2FNQ, 1U5U experimental model PDB 1U5U PDB entries 2FNQ, 1U5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 The drops were prepared with 2:1:1 mixtures of protein (5 mg/mL in 4 mM CaCl2), detergent (1.8 mM Triton X-100), and precipitant (16% PEG 3350, 4% Tacsimate pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.73 54.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 235.52 α = 90 b = 77.493 β = 112.45 c = 157.966 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 1.38000 CAMD GCPCC
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 3.5 39.2 98.2 0.135 3.4 32748 -3
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 3.5 3.63 86.8 0.364 1.84 2.6 2833
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 entries 2FNQ, 1U5U 3.51 20.86 30961 1644 98.09 0.27513 0.27264 0.2606 0.32191 0.3028 RANDOM 2.001
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] -1.45 -4.14 -0.56 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.532 r_dihedral_angle_4_deg 18.671 r_dihedral_angle_3_deg 18.552 r_dihedral_angle_1_deg 5.509 r_angle_refined_deg 1.234 r_symmetry_vdw_refined 0.349 r_nbtor_refined 0.317 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.532 r_dihedral_angle_4_deg 18.671 r_dihedral_angle_3_deg 18.552 r_dihedral_angle_1_deg 5.509 r_angle_refined_deg 1.234 r_symmetry_vdw_refined 0.349 r_nbtor_refined 0.317 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.082 r_symmetry_hbond_refined 0.08 r_metal_ion_refined 0.048 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 16130 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing