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Crystal structure of trypsin at 125 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, HANGING DROP 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.25 45.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.282 α = 90 b = 58.206 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 125 CMOS BRUKER PHOTON 100 2023-11-02 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 1.498 23.94 98.94 0.837 15.39 10 34191
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 23.93 0.837
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 1.498 23.94 34191 1705 98.929 0.186 0.185 0.2098 0.2093 10.235
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] -0.022 -0.054 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.211 r_dihedral_angle_6_deg 13.137 r_dihedral_angle_3_deg 10.842 r_dihedral_angle_1_deg 7.2 r_lrange_it 5.156 r_lrange_other 4.535 r_scangle_it 2.795 r_scangle_other 2.795 r_scbond_it 1.868 r_scbond_other 1.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.211 r_dihedral_angle_6_deg 13.137 r_dihedral_angle_3_deg 10.842 r_dihedral_angle_1_deg 7.2 r_lrange_it 5.156 r_lrange_other 4.535 r_scangle_it 2.795 r_scangle_other 2.795 r_scbond_it 1.868 r_scbond_other 1.867 r_angle_refined_deg 1.72 r_mcangle_it 1.524 r_mcangle_other 1.523 r_dihedral_angle_other_2_deg 1.282 r_mcbond_it 1.031 r_mcbond_other 1.021 r_angle_other_deg 0.606 r_xyhbond_nbd_refined 0.283 r_nbd_refined 0.221 r_symmetry_nbd_other 0.198 r_symmetry_nbd_refined 0.194 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.141 r_metal_ion_refined 0.125 r_nbd_other 0.125 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 315 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing