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Crystal structure of trypsin at 175 Kelvin with benzamidine (duplicate)
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 2.26 45.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.429 α = 90 b = 58.291 β = 90 c = 66.529 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 1.487 25.532 97.46 0.764 11.43 10 34522
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 25.53 0.764
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 1.487 25.532 34522 1701 97.316 0.198 0.197 0.1973 0.2246 0.2251 13.269
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] -0.324 -0.055 0.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.59 r_dihedral_angle_6_deg 13.391 r_dihedral_angle_3_deg 11.439 r_dihedral_angle_1_deg 7.187 r_lrange_it 5.693 r_lrange_other 5.283 r_scangle_it 3.455 r_scangle_other 3.454 r_scbond_it 2.291 r_scbond_other 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.59 r_dihedral_angle_6_deg 13.391 r_dihedral_angle_3_deg 11.439 r_dihedral_angle_1_deg 7.187 r_lrange_it 5.693 r_lrange_other 5.283 r_scangle_it 3.455 r_scangle_other 3.454 r_scbond_it 2.291 r_scbond_other 2.29 r_mcangle_it 2.288 r_mcangle_other 2.287 r_angle_refined_deg 1.734 r_mcbond_it 1.529 r_mcbond_other 1.522 r_dihedral_angle_other_2_deg 1.265 r_angle_other_deg 0.61 r_symmetry_xyhbond_nbd_other 0.319 r_xyhbond_nbd_refined 0.265 r_symmetry_xyhbond_nbd_refined 0.263 r_symmetry_nbd_refined 0.232 r_nbd_refined 0.216 r_symmetry_nbd_other 0.199 r_nbd_other 0.194 r_metal_ion_refined 0.179 r_nbtor_refined 0.177 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.086 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 323 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing