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Crystal structure of acyl-coA oxidase1 from Yarrowia lipolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W07 pdbid 1W07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 PEG 3350, NaCit, Tacsimate
Crystal Properties Matthews coefficient Solvent content 2.17 43.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.884 α = 90 b = 167.884 β = 90 c = 95.313 γ = 90
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 270 Rh coated Torroidal Mirror 2015-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 50 99.1 0.127 0.142 0.062 14.9 4.6 45463
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 98.3 0.316 0.366 0.181 0.785 3.7
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 pdbid 1W07 2.5 32.95 43281 2182 99 0.1937 0.1827 0.1839 0.2534 0.2552 RANDOM 43.177
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] 0.03 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.389 r_dihedral_angle_4_deg 19.371 r_dihedral_angle_3_deg 19.07 r_dihedral_angle_1_deg 6.458 r_angle_refined_deg 1.497 r_angle_other_deg 0.847 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.389 r_dihedral_angle_4_deg 19.371 r_dihedral_angle_3_deg 19.07 r_dihedral_angle_1_deg 6.458 r_angle_refined_deg 1.497 r_angle_other_deg 0.847 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10800 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling Coot model building PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing