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Crystal structure of trypsin at 125 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, HANGING DROP 9.4 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.49 α = 90 b = 58.282 β = 90 c = 66.66 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 125 CMOS BRUKER PHOTON 100 2023-11-01 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 23.989 98.87 0.813 19.03 10 34353
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 23.97 0.813
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 23.989 34353 1708 98.869 0.192 0.1902 0.1986 0.2197 0.23 7.611
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] -0.073 0.062 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.968 r_dihedral_angle_2_deg 11.655 r_dihedral_angle_3_deg 11.555 r_dihedral_angle_1_deg 7.153 r_lrange_it 4.632 r_lrange_other 4.012 r_scangle_it 2.248 r_scangle_other 2.248 r_angle_refined_deg 1.703 r_dihedral_angle_other_2_deg 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.968 r_dihedral_angle_2_deg 11.655 r_dihedral_angle_3_deg 11.555 r_dihedral_angle_1_deg 7.153 r_lrange_it 4.632 r_lrange_other 4.012 r_scangle_it 2.248 r_scangle_other 2.248 r_angle_refined_deg 1.703 r_dihedral_angle_other_2_deg 1.59 r_scbond_it 1.438 r_scbond_other 1.437 r_mcangle_it 1.31 r_mcangle_other 1.31 r_mcbond_it 0.812 r_mcbond_other 0.808 r_angle_other_deg 0.613 r_xyhbond_nbd_refined 0.276 r_nbd_refined 0.218 r_symmetry_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.167 r_nbd_other 0.163 r_metal_ion_refined 0.141 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.084 r_symmetry_metal_ion_refined 0.025 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 309 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing