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Crystal structure of trypsin at 250 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 9.4 298 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.18 43.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.824 α = 90 b = 56.986 β = 90 c = 66.449 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 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 1.497 26.926 98.77 0.622 3.18 10 33256
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 26.91 0.622
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 26.926 33255 1650 98.944 0.183 0.1815 0.182 0.2058 0.206 15.2
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] 0.361 -0.002 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.327 r_dihedral_angle_3_deg 11.991 r_dihedral_angle_2_deg 11.815 r_dihedral_angle_1_deg 7.331 r_lrange_it 6.643 r_lrange_other 6.39 r_scangle_it 4.222 r_scangle_other 4.222 r_mcangle_other 3.141 r_mcangle_it 3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.327 r_dihedral_angle_3_deg 11.991 r_dihedral_angle_2_deg 11.815 r_dihedral_angle_1_deg 7.331 r_lrange_it 6.643 r_lrange_other 6.39 r_scangle_it 4.222 r_scangle_other 4.222 r_mcangle_other 3.141 r_mcangle_it 3.14 r_scbond_it 2.857 r_scbond_other 2.855 r_mcbond_it 2.011 r_mcbond_other 2.011 r_angle_refined_deg 1.75 r_dihedral_angle_other_2_deg 1.721 r_angle_other_deg 0.628 r_xyhbond_nbd_refined 0.349 r_symmetry_nbd_refined 0.224 r_nbd_other 0.216 r_nbd_refined 0.213 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.112 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.026 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 168 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SCALA data scaling MOLREP phasing