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Crystal Structure of Thermomyces lanuginosa Lipase with acyl intermediate: space group I222
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 reservoirs of 0.6 ml and drop volumes of 6 ul. Reservoirs were 20% PEG 3350 with 0.1 M HEPES at pH 6.0. Drops were equal amounts of the reservoir and a 30 mg/ml stock protein solution. The solution was the raw growth broth for the Aspergillus expression system and the protein was not otherwise purified,
Crystal Properties Matthews coefficient Solvent content 2.03 39.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.865 α = 90 b = 85.268 β = 90 c = 86.741 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 173 PIXEL DECTRIS EIGER X 16M 2019-12-18 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 1.45 61 99.9 0.334 0.336 0.337 0.39 0.997 10.4 62.8 46198 23.17
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 1.45 1.47 97.8 3.6 3.7 3.7 0.58 0.29 0.6 38.7
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 1.45 60.81 1.37 46144 2287 99.86 0.1641 0.1605 0.1607 0.2352 0.2351 41.04
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 15.4109 f_angle_d 1.2529 f_chiral_restr 0.0834 f_plane_restr 0.0107 f_bond_d 0.0104
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2071 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 158
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing