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Soybean lipoxygenase-1 - re-refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 PEG 3350, SODIUM ACETATE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.9 α = 90 b = 94 β = 90.1 c = 49.9 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 CUSTOM-MADE 1994-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.908 CHESS A1
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 1.4 40 96 0.037 0.037 35.7 6.8 161029 161029 23.4
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) 1.4 1.42 91.6 0.343 0.343 3
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 FOURIER SYNTHESIS THROUGHOUT 1F8N 1.4 40 143562 143562 7559 87.97 0.15005 0.15005 0.14906 0.16866 0.183 RANDOM 19.13
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] -0.23 0.02 -0.14 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.754 r_dihedral_angle_4_deg 15.008 r_dihedral_angle_3_deg 11.609 r_dihedral_angle_1_deg 6.202 r_angle_other_deg 4.254 r_scangle_it 4.117 r_scbond_it 2.598 r_angle_refined_deg 1.724 r_mcangle_it 1.7 r_mcbond_it 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.754 r_dihedral_angle_4_deg 15.008 r_dihedral_angle_3_deg 11.609 r_dihedral_angle_1_deg 6.202 r_angle_other_deg 4.254 r_scangle_it 4.117 r_scbond_it 2.598 r_angle_refined_deg 1.724 r_mcangle_it 1.7 r_mcbond_it 1 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 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 6529 Nucleic Acid Atoms Solvent Atoms 1008 Heterogen Atoms 21
Software Software Software Name Purpose CHESS_A1 data collection HKL-3000 phasing REFMAC refinement Coot model building DENZO data reduction SCALEPACK data scaling REFMAC phasing