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Crystal structure of trypsin at 125 Kelvin with benzamidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.4 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.27 45.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.517 α = 90 b = 58.296 β = 90 c = 66.716 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 125 CMOS BRUKER PHOTON 100 2023-11-02 M LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER TURBO X-RAY SOURCE 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 24.7 99.34 0.659 9.35 10 34687
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 24.7 0.659
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 24.7 34687 1753 99.341 0.156 0.1543 0.154 0.1848 0.1859 8.844
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] 0.007 0.005 -0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.425 r_dihedral_angle_3_deg 12.166 r_dihedral_angle_2_deg 9.173 r_dihedral_angle_1_deg 7.103 r_lrange_it 5.013 r_lrange_other 4.469 r_scangle_it 2.802 r_scangle_other 2.801 r_scbond_it 1.936 r_scbond_other 1.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.425 r_dihedral_angle_3_deg 12.166 r_dihedral_angle_2_deg 9.173 r_dihedral_angle_1_deg 7.103 r_lrange_it 5.013 r_lrange_other 4.469 r_scangle_it 2.802 r_scangle_other 2.801 r_scbond_it 1.936 r_scbond_other 1.936 r_angle_refined_deg 1.664 r_mcangle_it 1.649 r_mcangle_other 1.649 r_dihedral_angle_other_2_deg 1.29 r_mcbond_it 1.07 r_mcbond_other 1.067 r_angle_other_deg 0.586 r_nbd_refined 0.215 r_symmetry_nbd_other 0.199 r_nbd_other 0.194 r_xyhbond_nbd_refined 0.182 r_symmetry_nbd_refined 0.18 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.122 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing