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Crystal structure of trypsin at 100 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 9.2 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.296 α = 90 b = 58.149 β = 90 c = 66.462 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 2023-11-01 M SINGLE WAVELENGTH
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 1.497 24.611 99.33 0.8797 17.53 10 34353
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 24.61 0.8797
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 1.497 24.611 34353 1742 99.329 0.157 0.1552 0.155 0.1846 0.1846 8.868
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] -0.003 -0.001 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.48 r_dihedral_angle_3_deg 11.888 r_dihedral_angle_2_deg 10.456 r_dihedral_angle_1_deg 7.196 r_lrange_it 4.696 r_lrange_other 4.164 r_scangle_it 2.79 r_scangle_other 2.788 r_scbond_other 1.957 r_scbond_it 1.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.48 r_dihedral_angle_3_deg 11.888 r_dihedral_angle_2_deg 10.456 r_dihedral_angle_1_deg 7.196 r_lrange_it 4.696 r_lrange_other 4.164 r_scangle_it 2.79 r_scangle_other 2.788 r_scbond_other 1.957 r_scbond_it 1.956 r_angle_refined_deg 1.679 r_mcangle_it 1.576 r_mcangle_other 1.576 r_dihedral_angle_other_2_deg 1.375 r_mcbond_it 1.041 r_mcbond_other 1.027 r_angle_other_deg 0.581 r_nbd_other 0.224 r_nbd_refined 0.21 r_symmetry_nbd_refined 0.204 r_symmetry_nbd_other 0.197 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.17 r_metal_ion_refined 0.116 r_symmetry_nbtor_other 0.086 r_chiral_restr 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 311 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing