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Crystal structure of trypsin at 175 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 45.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.325 α = 90 b = 58.226 β = 90 c = 66.254 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 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 1.49 23.085 94.17 0.652 10.91 10 33103
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 23.07 0.6521
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 1.491 23.085 33103 1628 94.688 0.237 0.235 0.242 0.2673 0.2726 9.37
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] -0.127 0.023 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.009 r_dihedral_angle_6_deg 13.1 r_dihedral_angle_3_deg 10.978 r_dihedral_angle_1_deg 7.262 r_lrange_it 4.955 r_lrange_other 4.081 r_scangle_it 2.44 r_scangle_other 2.44 r_mcangle_it 1.761 r_mcangle_other 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.009 r_dihedral_angle_6_deg 13.1 r_dihedral_angle_3_deg 10.978 r_dihedral_angle_1_deg 7.262 r_lrange_it 4.955 r_lrange_other 4.081 r_scangle_it 2.44 r_scangle_other 2.44 r_mcangle_it 1.761 r_mcangle_other 1.76 r_angle_refined_deg 1.715 r_scbond_it 1.583 r_scbond_other 1.582 r_mcbond_it 1.105 r_mcbond_other 1.104 r_dihedral_angle_other_2_deg 1.089 r_angle_other_deg 0.584 r_xyhbond_nbd_refined 0.282 r_nbd_refined 0.21 r_symmetry_nbd_other 0.203 r_nbd_other 0.201 r_symmetry_xyhbond_nbd_refined 0.2 r_symmetry_nbd_refined 0.195 r_nbtor_refined 0.176 r_metal_ion_refined 0.152 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.017 r_gen_planes_refined 0.01 r_bond_refined_d 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 295 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing