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Crystal Structure of Bovine Pancreatic Trypsin in Complex with Pyridoxal
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, HANGING DROP 7.5 293 0.1 M HEPES (pH =7.5), 0.1-0.4 M Li2SO4, and PEG 16%
Crystal Properties Matthews coefficient Solvent content 2.23 44.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.559 α = 90 b = 58.123 β = 90 c = 65.626 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS BRUKER PHOTON 100 2023-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 VENTURE 1.5406
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 2 20.99 99.9 0.088 14.8 3.4 14645
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2 0.368 3
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 20.99 13914 690 99.79 0.17105 0.16799 0.1799 0.23196 0.2332 RANDOM 11.07
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] -0.47 0.26 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.242 r_dihedral_angle_4_deg 17.956 r_dihedral_angle_3_deg 13.974 r_dihedral_angle_1_deg 7.886 r_long_range_B_refined 5.209 r_long_range_B_other 4.868 r_scangle_other 1.774 r_mcangle_it 1.616 r_mcangle_other 1.615 r_angle_refined_deg 1.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.242 r_dihedral_angle_4_deg 17.956 r_dihedral_angle_3_deg 13.974 r_dihedral_angle_1_deg 7.886 r_long_range_B_refined 5.209 r_long_range_B_other 4.868 r_scangle_other 1.774 r_mcangle_it 1.616 r_mcangle_other 1.615 r_angle_refined_deg 1.518 r_angle_other_deg 1.361 r_scbond_it 1.1 r_scbond_other 1.095 r_mcbond_it 0.959 r_mcbond_other 0.959 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 282 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction Aimless data scaling MOLREP phasing