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Crystal structure of trypsin at 275 Kelvin with benzamidine (duplicate)
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 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.258 α = 90 b = 57.015 β = 90 c = 66.971 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 275 PIXEL Bruker PHOTON II 2023-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER X8 PROTEUM 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 1.491 25.157 98.58 0.743 1.57 10 34045
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 25.14 0.743
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.491 25.157 34045 1687 98.521 0.24 0.2392 0.2641 0.2261 12.081
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] -0.398 0.421 -0.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.764 r_dihedral_angle_3_deg 12.721 r_dihedral_angle_2_deg 11.221 r_dihedral_angle_1_deg 7.535 r_lrange_it 5.197 r_lrange_other 4.928 r_scangle_it 3.221 r_scangle_other 3.22 r_mcangle_it 2.42 r_mcangle_other 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.764 r_dihedral_angle_3_deg 12.721 r_dihedral_angle_2_deg 11.221 r_dihedral_angle_1_deg 7.535 r_lrange_it 5.197 r_lrange_other 4.928 r_scangle_it 3.221 r_scangle_other 3.22 r_mcangle_it 2.42 r_mcangle_other 2.42 r_scbond_it 2.072 r_scbond_other 2.071 r_angle_refined_deg 1.619 r_mcbond_it 1.448 r_mcbond_other 1.447 r_dihedral_angle_other_2_deg 1.106 r_angle_other_deg 0.58 r_xyhbond_nbd_refined 0.408 r_nbd_refined 0.208 r_symmetry_nbd_other 0.201 r_nbd_other 0.187 r_nbtor_refined 0.173 r_metal_ion_refined 0.161 r_symmetry_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.08 r_symmetry_metal_ion_refined 0.069 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 129 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing