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Expression, crystallization and three-dimensional structure of the catalytic domain of human plasma kallikrein: Implications for structure-based design of protease inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P57 hepsin, PDB ENTRY 1P57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 0.5 microliter of the protein solution and 0.5 microliter of the reservoir solution (25% PEG 6000 , 0.10 M MES pH 6.5)., VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.886 α = 90 b = 63.19 β = 90 c = 50.313 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 138 CCD ADSC QUANTUM 315 2004-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 20 99.3 0.049 24.4 6.9 22313 22313
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT hepsin, PDB ENTRY 1P57 1.85 7 21184 21184 2123 99.4 0.2211 0.2211 0.221 0.2129 0.283 0.2133 RANDOM
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 x_dihedral_angle_d 26.6 x_angle_deg 3.2 x_bond_d 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2321 Nucleic Acid Atoms Solvent Atoms 642 Heterogen Atoms 18
Software Software Software Name Purpose DENZO data reduction XTALVIEW refinement X-PLOR refinement SCALEPACK data scaling