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Crystal structure of trypsin with its substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SY3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.1 M HEPES (pH=7.8), 16% PEG 3350, and 0.1-0.4 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.116 α = 90 b = 131.116 β = 90 c = 71.424 γ = 120
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 Bruker PHOTON II 2021-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.6406
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 2.3 16.83 99.7 0.096 0.99 19.2 5.6 10553
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 2.3 2.3 100 0.249 0.95 11.2 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6SY3 2.3 16.83 10005 542 99.62 0.14833 0.1456 0.1604 0.19782 0.2039 RANDOM 12.216
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.016 r_dihedral_angle_3_deg 14.32 r_dihedral_angle_1_deg 7.848 r_dihedral_angle_4_deg 7.117 r_long_range_B_refined 4.783 r_long_range_B_other 4.782 r_scangle_other 2.449 r_angle_refined_deg 1.578 r_mcangle_other 1.539 r_mcangle_it 1.531
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.016 r_dihedral_angle_3_deg 14.32 r_dihedral_angle_1_deg 7.848 r_dihedral_angle_4_deg 7.117 r_long_range_B_refined 4.783 r_long_range_B_other 4.782 r_scangle_other 2.449 r_angle_refined_deg 1.578 r_mcangle_other 1.539 r_mcangle_it 1.531 r_scbond_it 1.511 r_scbond_other 1.51 r_angle_other_deg 1.314 r_mcbond_it 0.914 r_mcbond_other 0.897 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction Aimless data scaling MOLREP phasing