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Crystal structure of trypsin at 275 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 2.33 47.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.532 α = 90 b = 58.82 β = 90 c = 67.803 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 SINGLE WAVELENGTH
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 1.497 24.195 97.24 0.714 4.78 10 34873
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 24.18 0.714
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 1.497 24.195 34873 1625 97.269 0.254 0.2523 0.2567 0.2852 0.2893 16.182
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] 0.136 0.681 -0.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.113 r_dihedral_angle_3_deg 12.736 r_dihedral_angle_2_deg 9.199 r_dihedral_angle_1_deg 7.132 r_lrange_it 5.567 r_lrange_other 5.391 r_scangle_it 3.909 r_scangle_other 3.909 r_scbond_it 2.541 r_scbond_other 2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.113 r_dihedral_angle_3_deg 12.736 r_dihedral_angle_2_deg 9.199 r_dihedral_angle_1_deg 7.132 r_lrange_it 5.567 r_lrange_other 5.391 r_scangle_it 3.909 r_scangle_other 3.909 r_scbond_it 2.541 r_scbond_other 2.54 r_mcangle_it 2.424 r_mcangle_other 2.423 r_angle_refined_deg 1.604 r_mcbond_it 1.585 r_mcbond_other 1.583 r_dihedral_angle_other_2_deg 0.881 r_angle_other_deg 0.56 r_xyhbond_nbd_refined 0.342 r_nbd_other 0.252 r_symmetry_xyhbond_nbd_refined 0.23 r_nbd_refined 0.207 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.171 r_metal_ion_refined 0.152 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.074 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 160 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing