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Crystal structure of trypsin at 175 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, HANGING DROP 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.27 45.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.441 α = 90 b = 58.303 β = 90 c = 66.74 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 175 CMOS BRUKER PHOTON 100 2023-11-04 M LAUE
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 1.495 23.15 98.78 0.798 12.1 10 34642
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 23.15 0.798
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 1.495 23.146 34642 1752 98.78 0.185 0.1836 0.1834 0.2182 0.2179 12.171
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] -0.001 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.846 r_dihedral_angle_2_deg 12.404 r_dihedral_angle_3_deg 11.531 r_dihedral_angle_1_deg 7.156 r_lrange_it 4.837 r_lrange_other 4.48 r_scangle_it 2.943 r_scangle_other 2.942 r_scbond_it 2.066 r_scbond_other 2.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.846 r_dihedral_angle_2_deg 12.404 r_dihedral_angle_3_deg 11.531 r_dihedral_angle_1_deg 7.156 r_lrange_it 4.837 r_lrange_other 4.48 r_scangle_it 2.943 r_scangle_other 2.942 r_scbond_it 2.066 r_scbond_other 2.065 r_mcangle_it 1.857 r_mcangle_other 1.856 r_angle_refined_deg 1.626 r_mcbond_it 1.278 r_mcbond_other 1.272 r_dihedral_angle_other_2_deg 1.241 r_angle_other_deg 0.553 r_nbd_refined 0.209 r_symmetry_nbd_other 0.196 r_symmetry_nbd_refined 0.185 r_nbd_other 0.184 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.17 r_xyhbond_nbd_refined 0.164 r_metal_ion_refined 0.117 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.079 r_gen_planes_refined 0.011 r_bond_refined_d 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 300 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing