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Crystal structure of trypsin at 250 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 2.17 43.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.884 α = 90 b = 56.774 β = 90 c = 66.223 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 250 CMOS BRUKER PHOTON 100 2023-11-07 M LAUE
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 1.484 23.494 95.61 0.822 8.96 10 32789
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 23.49 0.822
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 1.484 23.494 32789 1670 95.614 0.224 0.2221 0.2312 0.2554 0.2614 13.223
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] 0.003 0.016 -0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.377 r_dihedral_angle_3_deg 12.693 r_dihedral_angle_2_deg 11.679 r_dihedral_angle_1_deg 7.079 r_lrange_it 6.791 r_lrange_other 6.511 r_scangle_it 3.133 r_scangle_other 3.132 r_scbond_it 2.094 r_scbond_other 2.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.377 r_dihedral_angle_3_deg 12.693 r_dihedral_angle_2_deg 11.679 r_dihedral_angle_1_deg 7.079 r_lrange_it 6.791 r_lrange_other 6.511 r_scangle_it 3.133 r_scangle_other 3.132 r_scbond_it 2.094 r_scbond_other 2.092 r_mcangle_it 1.949 r_mcangle_other 1.949 r_angle_refined_deg 1.538 r_mcbond_it 1.281 r_mcbond_other 1.281 r_dihedral_angle_other_2_deg 1.173 r_angle_other_deg 0.556 r_xyhbond_nbd_refined 0.224 r_symmetry_nbd_other 0.211 r_nbd_refined 0.209 r_nbd_other 0.207 r_symmetry_nbd_refined 0.2 r_nbtor_refined 0.181 r_metal_ion_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.157 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.076 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_symmetry_xyhbond_nbd_other 0.003 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 180 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing