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Crystal Structure of Thermomyces lanuginosa Lipase With Bound 1,3 diacylglycrol and Fatty Acid Acyl intermediates: Monoclinic Crystals
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 Crystallized by sitting drop vapor diffusion with 0.6 ml reservoirs and drop volumes 6 ul. Drops consisted of equal volumes of the reservoir and the protein stock solution. The reservoirs were 20% w/v PEG 3350 with 0.1 M HEPES buffer. The protein was in the growth broth of the aspergillum expression system and was not further purified. The stock protein concentration was 30 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.929 α = 90 b = 89.937 β = 94.488 c = 123.422 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 173 PIXEL DECTRIS EIGER X 16M 2024-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.43 77 99.7 0.158 0.146 0.163 0.36 0.998 9.1 19.2 307462 21.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.47 98.8 5.69 4.85 6.1 1.66 0.26 0.4 13.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.43 76.69 1.33 306740 15362 99.43 0.1326 0.1301 0.1311 0.1811 0.1815 32.28
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.8319 f_angle_d 1.0123 f_chiral_restr 0.0784 f_plane_restr 0.0088 f_bond_d 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12423 Nucleic Acid Atoms Solvent Atoms 2359 Heterogen Atoms 833
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing