☰ Navigation Tabs
Crystal structure of trypsin at 275 Kelvin with benzamidine
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 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 = 54.44 α = 90 b = 57.339 β = 90 c = 67.134 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 275 PIXEL Bruker PHOTON II 2023-11-08 M LAUE
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 1.491 21.8 95.47 0.804 13.8 10 33357
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 21.8 0.804
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 21.8 33357 1669 95.469 0.228 0.2262 0.2266 0.273 0.2743 19.66
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] 0.013 -0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.949 r_dihedral_angle_3_deg 13.781 r_dihedral_angle_2_deg 7.65 r_dihedral_angle_1_deg 7.017 r_lrange_it 5.714 r_lrange_other 5.371 r_scangle_it 3.745 r_scangle_other 3.745 r_scbond_it 2.521 r_scbond_other 2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.949 r_dihedral_angle_3_deg 13.781 r_dihedral_angle_2_deg 7.65 r_dihedral_angle_1_deg 7.017 r_lrange_it 5.714 r_lrange_other 5.371 r_scangle_it 3.745 r_scangle_other 3.745 r_scbond_it 2.521 r_scbond_other 2.52 r_mcangle_it 2.391 r_mcangle_other 2.39 r_mcbond_it 1.627 r_mcbond_other 1.626 r_angle_refined_deg 1.467 r_angle_other_deg 0.506 r_xyhbond_nbd_refined 0.362 r_nbd_other 0.213 r_nbd_refined 0.212 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.134 r_symmetry_nbd_refined 0.129 r_metal_ion_refined 0.116 r_dihedral_angle_other_2_deg 0.089 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.071 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 120 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing