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X-ray crystal structure of LeACX1, an acyl-CoA oxidase from Lycopersicon esculentum (tomato)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 296 10% 2-methyl-2,4-pentanediol, 7% PEG 6000, 100 mM Tris, 1 mM acetyl-CoA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.89 57.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.2 α = 90 b = 240.33 β = 90 c = 89.3 γ = 90
Symmetry Space Group P 21 21 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 MARRESEARCH 2004-02-28 M SINGLE WAVELENGTH 2 1 CCD MARRESEARCH 2004-03-20
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 1.0 APS 32-ID 2 SYNCHROTRON APS BEAMLINE 32-ID 1.0 APS 32-ID
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 2.7 30 95.4 0.092 12.2 6 64138 50.87
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 2.7 2.77 99.8 0.374
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.74 30 63839 3221 92.86 0.214 0.212 0.2049 0.267 0.2613 RANDOM 69.077
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] -4.83 2.47 2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.472 r_dihedral_angle_4_deg 20.889 r_dihedral_angle_3_deg 19.783 r_dihedral_angle_1_deg 6.595 r_scangle_it 3.448 r_scbond_it 2.163 r_angle_refined_deg 1.863 r_mcangle_it 1.254 r_mcbond_it 0.736 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.472 r_dihedral_angle_4_deg 20.889 r_dihedral_angle_3_deg 19.783 r_dihedral_angle_1_deg 6.595 r_scangle_it 3.448 r_scbond_it 2.163 r_angle_refined_deg 1.863 r_mcangle_it 1.254 r_mcbond_it 0.736 r_nbtor_refined 0.318 r_nbd_refined 0.251 r_symmetry_vdw_refined 0.213 r_symmetry_hbond_refined 0.207 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.125 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14754 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 159
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction