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Crystal structure of human mature meprin beta in complex with the specific inhibitor MWT-S-270
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GWN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 286 Protein was mixed with inhibitor in a molar ratio of 1 to 1.2 to a final protein concentration of 8 mg/mL in 30 mM Tris, 100 mM sodium chloride, pH 7.6.
200 nL protein/inhibitor was mixed with 200 nL praezipitation buffer and equilibrated against 55 micro Liter of praezipitation buffer, containing 25 percent (w/v) PEG 4000 and 30 percent (v/v) ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.92 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.25 α = 90 b = 72.44 β = 118.43 c = 135.47 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 93 CCD RIGAKU SATURN 944+ 2017-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.41 44.969 99.1 0.119 0.131 0.997 11.48 5.64 103582 49.027
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.48 95.5 1.019 1.129 0.746 1.79 5.318
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 4gwn 2.413 44.969 1.34 103497 5193 99.21 0.2004 0.1985 0.2013 0.236 0.2388 55.5223
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 8542 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 791
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction