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Crystal structure of monoacylglycerol lipase with BODIPY labeled probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PE6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 8 %v/v 1-Propan
0.1 M MES pH 6.5
12 %w/v PEG MME 5K
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.896 α = 90 b = 127.245 β = 90 c = 62.206 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2024-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.885603 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.41 72.87 99.9 0.093 0.997 8.97 10.36 68084 18.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.5 0.99 0.552
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 1.41 36.16 1.33 67897 3323 99.63 0.1586 0.1573 0.1586 0.1846 0.1856 28.38
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 13.8513 f_angle_d 0.8378 f_chiral_restr 0.0765 f_plane_restr 0.007 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2244 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 81
Software Software Software Name Purpose PHENIX refinement XDS data reduction SADABS data scaling PHASER phasing