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Crystal structure of trypsin at 300 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 = 54.214 α = 90 b = 57.413 β = 90 c = 66.567 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 300 PIXEL Bruker PHOTON II 2023-11-09 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 1.483 25.443 95.1 0.743 8.8 10 34788
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 25.41 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.484 25.443 33339 1680 95.067 0.218 0.2164 0.2244 0.2446 0.2494 22.881
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] -0.943 0.009 0.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.097 r_dihedral_angle_6_deg 12.787 r_dihedral_angle_1_deg 7.201 r_lrange_it 6.194 r_lrange_other 6.142 r_dihedral_angle_2_deg 5.96 r_scangle_it 4.888 r_scangle_other 4.888 r_scbond_it 3.232 r_scbond_other 3.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.097 r_dihedral_angle_6_deg 12.787 r_dihedral_angle_1_deg 7.201 r_lrange_it 6.194 r_lrange_other 6.142 r_dihedral_angle_2_deg 5.96 r_scangle_it 4.888 r_scangle_other 4.888 r_scbond_it 3.232 r_scbond_other 3.23 r_mcangle_it 3.091 r_mcangle_other 3.09 r_mcbond_it 2.074 r_mcbond_other 2.074 r_angle_refined_deg 1.638 r_angle_other_deg 0.587 r_xyhbond_nbd_refined 0.382 r_dihedral_angle_other_2_deg 0.312 r_symmetry_nbd_refined 0.259 r_nbd_refined 0.208 r_symmetry_nbd_other 0.206 r_symmetry_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.176 r_metal_ion_refined 0.162 r_nbd_other 0.16 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.085 r_symmetry_xyhbond_nbd_other 0.022 r_bond_refined_d 0.008 r_gen_planes_refined 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 86 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing