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Crystal Structure of Thermomyces lanuginosa Lipase With Bound 1,3 Diacylglycerol and Fatty Acid Acyl Intermediates: Space Group H32
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 5 298 Vapor diffusion in sitting drops. reservoirs 0.6 ml and drop size of 6 ul. reservoir 12 % Peg 3350 buffered with 0.1 M HEPES. Drop initially 3 ul of a 30 mg/ml protein stack solution plus 3 ul of reservoir. Time for crystal formation about 3 to 5 days. The protein was in the growth broth of the aspergillum expression system and was not purified
Crystal Properties Matthews coefficient Solvent content 2.13 42.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.373 α = 90 b = 76.373 β = 90 c = 241.551 γ = 120
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 STFC Large Pixel Detector 2024-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.00 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.3 85 87.92 0.49 0.05 0.49 1 8.7 31 58354 13.9
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 1.3 1.333 14.4 0.36 0.29 0.461 0.205 0.81 2.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.3 80.52 1.37 58354 2865 87.92 0.1244 0.1227 0.1233 0.1566 0.1564 random selection 34.03
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 16.6057 f_angle_d 1.6096 f_chiral_restr 0.094 f_plane_restr 0.0128 f_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2008 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 384
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing