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Cationic trypsin in complex with a derivative of benzamidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.1% (NH4)2SO4
0.1% imidazole
22% PEG 8000
0.1% NaN3
Crystal Properties Matthews coefficient Solvent content 2.35 74.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.803 α = 90 b = 54.803 β = 90 c = 108.558 γ = 120
Symmetry Space Group P 31 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 IMAGE PLATE MAR scanner 345 mm plate Signally blended Si111 crystal 2020-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.29 47.5 99.9 0.05 1 26.12 9.7 48302 12.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.37 99.7 0.54 0.93 3.68 9.4
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 FREE R-VALUE 5MNK 1.29 23.73 1.37 48274 2414 99.89 0.1283 0.1274 0.1272 0.1446 0.1454 15.96
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 13.282 f_angle_d 0.9366 f_chiral_restr 0.0841 f_plane_restr 0.0057 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1603 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 53
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing Coot model building