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Crystal structure of trypsin at 150 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, SITTING DROP 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.13 42.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.658 α = 90 b = 57.15 β = 90 c = 64.795 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 150 CMOS BRUKER PHOTON 100 2023-11-03 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 1.496 22.751 99.16 0.877 15.54 10 32548
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 22.75 0.877
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 1.496 22.751 32548 1590 99.162 0.178 0.1766 0.1765 0.2136 0.2133 12.505
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] -0.004 -0.009 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.762 r_dihedral_angle_3_deg 12.925 r_dihedral_angle_2_deg 12.413 r_dihedral_angle_1_deg 7.319 r_lrange_it 5.018 r_lrange_other 5.017 r_scangle_it 3.162 r_scangle_other 3.161 r_scbond_it 2.192 r_scbond_other 2.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.762 r_dihedral_angle_3_deg 12.925 r_dihedral_angle_2_deg 12.413 r_dihedral_angle_1_deg 7.319 r_lrange_it 5.018 r_lrange_other 5.017 r_scangle_it 3.162 r_scangle_other 3.161 r_scbond_it 2.192 r_scbond_other 2.192 r_mcangle_it 2.146 r_mcangle_other 2.146 r_angle_refined_deg 1.618 r_dihedral_angle_other_2_deg 1.491 r_mcbond_it 1.411 r_mcbond_other 1.411 r_angle_other_deg 0.568 r_symmetry_xyhbond_nbd_refined 0.26 r_nbd_other 0.22 r_nbd_refined 0.202 r_symmetry_nbd_other 0.196 r_symmetry_nbd_refined 0.195 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.173 r_metal_ion_refined 0.148 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.081 r_symmetry_xyhbond_nbd_other 0.048 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 313 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing