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Crystal structure of trypsin at 250 Kelvin with benzamidine (triplicate)
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 2.19 43.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.83 α = 90 b = 56.991 β = 90 c = 66.463 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 250 CMOS BRUKER PHOTON 100 2023-11-07 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 26.929 98.68 0.863 11.05 10 33223
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 26.91 0.863
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 26.929 33223 1649 98.825 0.177 0.176 0.1764 0.1993 0.1992 14.726
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] 0.243 -0.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.931 r_dihedral_angle_6_deg 14.576 r_dihedral_angle_3_deg 12.672 r_dihedral_angle_1_deg 7.308 r_lrange_it 6.063 r_lrange_other 5.873 r_scangle_it 4.306 r_scangle_other 4.306 r_scbond_it 2.92 r_scbond_other 2.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.931 r_dihedral_angle_6_deg 14.576 r_dihedral_angle_3_deg 12.672 r_dihedral_angle_1_deg 7.308 r_lrange_it 6.063 r_lrange_other 5.873 r_scangle_it 4.306 r_scangle_other 4.306 r_scbond_it 2.92 r_scbond_other 2.918 r_mcangle_it 2.685 r_mcangle_other 2.685 r_dihedral_angle_other_2_deg 1.945 r_angle_refined_deg 1.814 r_mcbond_it 1.752 r_mcbond_other 1.751 r_angle_other_deg 0.652 r_xyhbond_nbd_refined 0.351 r_nbd_refined 0.208 r_symmetry_nbd_other 0.199 r_symmetry_xyhbond_nbd_refined 0.194 r_nbd_other 0.183 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.137 r_metal_ion_refined 0.125 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.011 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 176 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing