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Crystal structure of trypsin at 225 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 2.2 44.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.866 α = 90 b = 57.041 β = 90 c = 66.72 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 225 CMOS BRUKER PHOTON 100 2023-11-06 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 1.499 23.59 93.81 0.808 7.51 10 33354
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 23.58 0.808
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 1.499 23.59 33354 1652 99.073 0.193 0.1911 0.1912 0.2186 0.2188 13.447
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] -0.036 0.089 -0.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.692 r_dihedral_angle_6_deg 14.397 r_dihedral_angle_3_deg 11.589 r_dihedral_angle_1_deg 6.717 r_lrange_it 5.664 r_lrange_other 5.421 r_scangle_it 3.671 r_scangle_other 3.671 r_scbond_it 2.379 r_scbond_other 2.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.692 r_dihedral_angle_6_deg 14.397 r_dihedral_angle_3_deg 11.589 r_dihedral_angle_1_deg 6.717 r_lrange_it 5.664 r_lrange_other 5.421 r_scangle_it 3.671 r_scangle_other 3.671 r_scbond_it 2.379 r_scbond_other 2.377 r_mcangle_it 2.371 r_mcangle_other 2.37 r_angle_refined_deg 1.718 r_mcbond_it 1.491 r_mcbond_other 1.489 r_dihedral_angle_other_2_deg 1.011 r_angle_other_deg 0.608 r_xyhbond_nbd_refined 0.323 r_symmetry_xyhbond_nbd_refined 0.248 r_nbd_refined 0.22 r_symmetry_nbd_other 0.204 r_nbd_other 0.18 r_nbtor_refined 0.175 r_symmetry_nbd_refined 0.162 r_metal_ion_refined 0.127 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.032 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 193 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing