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Crystal structure of the catalytic region of human MASP-2 with specific inhibitor Compound S3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2.0 uL of protein (0.62 mg/mL MASP2) was mixed with 2.0 uL of reservoir solution (0.1 M Tris-HCl pH 7.6, 0.16 M NaCl, 30% (w/v) PEG 6000, 10% (v/v) glycerol) and equilibrated against reservoir at 20 C. Crystals were soaked in reservoir supplemented with 20% (v/v) glycerol and 0.5 mM Compound S3.
Crystal Properties Matthews coefficient Solvent content 2.15 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.65 α = 90 b = 41.11 β = 98.22 c = 103.13 γ = 90
Symmetry Space Group C 1 2 1
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 9M 2023-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95358 CLSI 08ID-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 2.36 35.95 99.66 0.1846 0.988 5.88 3.7 12638
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 2.36 2.44 1.655 0.281 0.92
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.36 35.95 12634 566 99.68 0.2 0.2001 0.2509 0.2517
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2436 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 69
Software Software Software Name Purpose xia2 data reduction xia2 data scaling PHASER phasing PHENIX refinement