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Crystal structure of trypsin at 100 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 2.24 45.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.095 α = 90 b = 58.074 β = 90 c = 66.573 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 100 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 24.531 92.47 0.7452 16.57 10 31751
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 24.42 0.7452
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 24.531 31751 1582 92.485 0.207 0.2058 0.2145 0.233 0.2429 7.867
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] 0.231 -0.178 -0.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.029 r_dihedral_angle_6_deg 14.385 r_dihedral_angle_3_deg 11.562 r_dihedral_angle_1_deg 7.101 r_lrange_it 5.052 r_lrange_other 4.488 r_scangle_it 2.245 r_scangle_other 2.245 r_angle_refined_deg 1.719 r_dihedral_angle_other_2_deg 1.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.029 r_dihedral_angle_6_deg 14.385 r_dihedral_angle_3_deg 11.562 r_dihedral_angle_1_deg 7.101 r_lrange_it 5.052 r_lrange_other 4.488 r_scangle_it 2.245 r_scangle_other 2.245 r_angle_refined_deg 1.719 r_dihedral_angle_other_2_deg 1.659 r_mcangle_it 1.441 r_mcangle_other 1.44 r_scbond_it 1.413 r_scbond_other 1.412 r_mcbond_it 0.882 r_mcbond_other 0.881 r_angle_other_deg 0.601 r_xyhbond_nbd_refined 0.3 r_symmetry_xyhbond_nbd_refined 0.269 r_nbd_refined 0.224 r_nbd_other 0.211 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.172 r_metal_ion_refined 0.155 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.084 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_symmetry_metal_ion_refined 0.006 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 268 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing