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Crystal structure of trypsin at 300 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 2.25 45.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.327 α = 90 b = 57.396 β = 90 c = 67.336 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 1.488 23.12 98.56 0.684 7.124 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 23.12 0.684
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 1.488 23.078 34788 1760 98.743 0.188 0.1861 0.1958 0.2261 0.2267 18.68
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] 0.272 -0.22 -0.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.855 r_dihedral_angle_3_deg 13.053 r_dihedral_angle_2_deg 10.845 r_dihedral_angle_1_deg 6.516 r_lrange_it 6.136 r_lrange_other 6.128 r_scangle_it 5.204 r_scangle_other 5.204 r_scbond_it 3.404 r_scbond_other 3.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.855 r_dihedral_angle_3_deg 13.053 r_dihedral_angle_2_deg 10.845 r_dihedral_angle_1_deg 6.516 r_lrange_it 6.136 r_lrange_other 6.128 r_scangle_it 5.204 r_scangle_other 5.204 r_scbond_it 3.404 r_scbond_other 3.402 r_mcangle_it 2.718 r_mcangle_other 2.717 r_mcbond_it 1.878 r_mcbond_other 1.875 r_angle_refined_deg 1.786 r_dihedral_angle_other_2_deg 0.778 r_angle_other_deg 0.648 r_xyhbond_nbd_refined 0.405 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_refined 0.209 r_symmetry_nbd_other 0.203 r_symmetry_nbd_refined 0.2 r_nbtor_refined 0.182 r_nbd_other 0.155 r_metal_ion_refined 0.143 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.089 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 80 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing