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Crystal structure of trypsin at 300 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 9.4 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.333 α = 90 b = 57.39 β = 90 c = 67.409 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 300 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 1.482 23.071 97.42 0.716 7.82 10 34783
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 23.07 0.716
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 1.482 23.071 34783 1754 97.423 0.204 0.2022 0.2121 0.2397 0.2452 18.287
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] 0.006 -0.01 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.735 r_dihedral_angle_3_deg 12.877 r_dihedral_angle_2_deg 11.22 r_dihedral_angle_1_deg 6.643 r_lrange_it 5.696 r_lrange_other 5.603 r_scangle_it 4.595 r_scangle_other 4.595 r_scbond_it 3.002 r_scbond_other 3.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.735 r_dihedral_angle_3_deg 12.877 r_dihedral_angle_2_deg 11.22 r_dihedral_angle_1_deg 6.643 r_lrange_it 5.696 r_lrange_other 5.603 r_scangle_it 4.595 r_scangle_other 4.595 r_scbond_it 3.002 r_scbond_other 3.001 r_mcangle_it 2.58 r_mcangle_other 2.579 r_mcbond_it 1.753 r_mcbond_other 1.751 r_angle_refined_deg 1.584 r_dihedral_angle_other_2_deg 0.709 r_angle_other_deg 0.552 r_xyhbond_nbd_refined 0.394 r_symmetry_nbd_refined 0.304 r_nbd_other 0.303 r_nbd_refined 0.218 r_symmetry_nbd_other 0.2 r_symmetry_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.181 r_metal_ion_refined 0.125 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.037 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 86 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing