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Crystal structure of Oryza sativa fatty acid alpha-dioxygenase Y379F with palmitic acid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 300 45% PEG 400, 0.2M lithium chloride, 0.1M sodium citrate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 3.15 60.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.887 α = 90 b = 130.202 β = 90 c = 188.173 γ = 90
Symmetry Space Group I 2 2 2
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 ADSC QUANTUM 210 2011-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.977 CHESS A1
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 1.96 107.07 99.9 0.063 25.2 5.8 64653 64653 -3 -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 1.96 1.99 99.4 0.566 2.8 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.96 107.07 64653 61133 3256 99.29 0.1582 0.1567 0.1696 0.18582 0.2001 RANDOM 32.663
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] 1.05 1.07 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.905 r_dihedral_angle_4_deg 16.998 r_dihedral_angle_3_deg 13.5 r_scangle_it 5.679 r_dihedral_angle_1_deg 5.647 r_scbond_it 3.704 r_mcangle_it 2.241 r_mcbond_it 1.308 r_angle_refined_deg 1.223 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.905 r_dihedral_angle_4_deg 16.998 r_dihedral_angle_3_deg 13.5 r_scangle_it 5.679 r_dihedral_angle_1_deg 5.647 r_scbond_it 3.704 r_mcangle_it 2.241 r_mcbond_it 1.308 r_angle_refined_deg 1.223 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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 4908 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 216
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling